From 13beabc9e2aa893448fa886d218c25287f22fc66 Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 15:42:11 -0600 Subject: [PATCH 01/17] adding mpx_yale --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index c0e8496..ea72526 100644 --- a/README.md +++ b/README.md @@ -230,7 +230,7 @@ params.minimum_depth = 10 The defaults for Cecret continue to be for SARS-CoV-2, but there are growing demands for a workflow for Monkeypox Virus. As such, there are a few parameters that might benefit the **End User**. ### Using the Monkeypox profile -There are three profiles for Monkeypox Virus sequencing : `mpx`, `mpx_idt` and `mpx_primalseq`. The `mpx` profile has some defaults for a metagenomic-type sequencing, while `mpx_idt` is for libraries prepped with [IDT](https://www.idtdna.com/)'s primers, and `mpx_primalseq` which has been [validated](https://www.medrxiv.org/content/10.1101/2022.10.14.22280783v1.full-text) with Illumina library prep methods and sequencing platforms. +There are three profiles for Monkeypox Virus sequencing : `mpx`, `mpx_idt`, `mpx_yale`, and `mpx_primalseq`. The `mpx` profile has some defaults for a metagenomic-type sequencing, while `mpx_idt` is for libraries prepped with [IDT](https://www.idtdna.com/)'s primers, and `mpx_primalseq` which has been [validated](https://www.medrxiv.org/content/10.1101/2022.10.14.22280783v1.full-text) with Illumina library prep methods and sequencing platforms. ``` # metagenomic nextflow run UPHL-BioNGS/Cecret -profile singularity,mpx @@ -238,6 +238,9 @@ nextflow run UPHL-BioNGS/Cecret -profile singularity,mpx # using IDT's primers nextflow run UPHL-BioNGS/Cecret -profile singularity,mpx_idt +# using primalseq with Yale's reference +nextflow run UPHL-BioNGS/Cecret -profile singularity,mpx_yale + # using Illumina library prep methods and sequencing platforms nextflow run UPHL-BioNGS/Cecret -profile singularity,mpx_primalseq ``` From c72ea0950031566a0a0fb4e47170f45708399615 Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 15:42:29 -0600 Subject: [PATCH 02/17] fix vadr results --- bin/combine_results.py | 35 ++++++++++++++++++++++------------- 1 file changed, 22 insertions(+), 13 deletions(-) diff --git a/bin/combine_results.py b/bin/combine_results.py index 25b8481..744bfb7 100755 --- a/bin/combine_results.py +++ b/bin/combine_results.py @@ -10,9 +10,9 @@ aci_file = 'aci_coverage_summary.csv' ampliconstats_file = 'ampliconstats.summary' samtools_coverage_file = 'samtools_coverage_summary.tsv' -pangolin_file = 'multiqc_data/multiqc_pangolin.txt' +pangolin_file = 'lineage_report.csv' pango_collapse_file = 'pango_collapse.csv' -nextclade_file = 'multiqc_data/multiqc_nextclade.txt' +nextclade_file = 'nextclade.csv' vadr_file = 'vadr.csv' fastp_file = 'multiqc_data/multiqc_general_stats.txt' fastq_names_file = 'fastq_names.csv' @@ -277,9 +277,17 @@ summary_df = summary_df.drop('sample', axis=1) columns = columns + ['samtools_meandepth_after_trimming', 'samtools_per_1X_coverage_after_trimming'] +def vadr_sample_name(s): + if s.count('.') >=1: + if len(s.split(".")[-1]) > 2: + return ''.join(s.split(".")[:-1]) + return s + if exists(vadr_file) : print("Getting results from vadr file " + vadr_file) vadr_df = pd.read_csv(vadr_file, dtype = str, usecols = ['name', 'p/f', 'model', 'alerts'], index_col= False) + vadr_df = vadr_df[vadr_df['name'] != 'name'] + vadr_df = vadr_df[vadr_df['name'] != 'seq'] vadr_df = vadr_df.add_prefix('vadr_') vadr_columns = list(vadr_df.columns) vadr_columns.remove('vadr_name') @@ -291,7 +299,8 @@ summary_df.drop('vadr_name', axis=1, inplace=True) columns = ['vadr_p/f'] + columns + vadr_columns else: - vadr_df['sample_match'] = vadr_df['vadr_name'].str.replace('Consensus_', '', regex = False).str.split(".").str[0] + vadr_df['sample_match'] = vadr_df['vadr_name'].str.replace('Consensus_', '', regex = False).apply(vadr_sample_name) + summary_df = pd.merge(summary_df, vadr_df, left_on = 'sample_id', right_on = 'sample_match', how = 'outer') summary_df['sample_id'].fillna(summary_df['sample_match'], inplace=True) summary_df.drop('vadr_name', axis=1, inplace=True) @@ -301,9 +310,9 @@ if exists(nextclade_file) : print("Getting results from nextclade file " + nextclade_file) - use_cols = ['Sample', 'clade', 'qc_overallstatus', 'qc_overallscore'] + use_cols = ['seqName', 'clade', 'qc.overallStatus', 'qc.overallScore'] - first = pd.read_table(nextclade_file, sep = '\t' , dtype = str, nrows=1) + first = pd.read_table(nextclade_file, sep = ';' , dtype = str, nrows=1) if 'clade_who' in first.columns: use_cols.append('clade_who') if 'outbreak' in first.columns: @@ -311,32 +320,32 @@ if 'lineage' in first.columns: use_cols.append('lineage') - nextclade_df = pd.read_table(nextclade_file, sep = '\t' , dtype = str, usecols = use_cols) + nextclade_df = pd.read_table(nextclade_file, sep = ';' , dtype = str, usecols = use_cols) nextclade_df=nextclade_df.add_prefix('nextclade_') nextclade_columns = list(nextclade_df.columns) - nextclade_df['sample_match'] = nextclade_df['nextclade_Sample'].str.replace('Consensus_', '', regex = False) - nextclade_columns.remove('nextclade_Sample') + nextclade_df['sample_match'] = nextclade_df['nextclade_seqName'].str.replace('Consensus_', '', regex = False).str.split(' ').str[0] + nextclade_columns.remove('nextclade_seqName') nextclade_columns.remove('nextclade_clade') summary_df = pd.merge(summary_df, nextclade_df, left_on = 'sample_id', right_on = 'sample_match', how = 'outer') summary_df['sample_id'].fillna(summary_df['sample_match'], inplace=True) - summary_df.drop('nextclade_Sample', axis=1, inplace=True) + summary_df.drop('nextclade_seqName', axis=1, inplace=True) summary_df.drop('sample_match', axis = 1, inplace = True ) columns = ['nextclade_clade'] + columns + nextclade_columns if exists(pangolin_file) : print("Getting results from pangolin file " + pangolin_file) - pangolin_df = pd.read_table(pangolin_file, dtype = str) + pangolin_df = pd.read_csv(pangolin_file, dtype = str) pangolin_df = pangolin_df.add_prefix('pangolin_') pangolin_columns = list(pangolin_df.columns) - pangolin_df['sample_match'] = pangolin_df['pangolin_Sample'].str.replace('Consensus_', '', regex= False) - pangolin_columns.remove('pangolin_Sample') + pangolin_df['sample_match'] = pangolin_df['pangolin_taxon'].str.replace('Consensus_', '', regex= False).str.split(' ').str[0] + pangolin_columns.remove('pangolin_taxon') pangolin_columns.remove('pangolin_lineage') summary_df = pd.merge(summary_df, pangolin_df, left_on = 'sample_id', right_on = 'sample_match', how = 'outer') summary_df['sample_id'].fillna(summary_df['sample_match'], inplace=True) - summary_df.drop('pangolin_Sample', axis=1, inplace=True) + summary_df.drop('pangolin_taxon', axis=1, inplace=True) summary_df.drop('sample_match', axis=1, inplace=True) columns = ['pangolin_lineage'] + columns + pangolin_columns From 181c9e5971430706a5b35d873d4030c6f5d6389b Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 15:42:47 -0600 Subject: [PATCH 03/17] fixed workflow version --- main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/main.nf b/main.nf index 01ed247..ae5dfe8 100644 --- a/main.nf +++ b/main.nf @@ -513,7 +513,7 @@ ch_reads.ifEmpty { println("No fastq or fastq.gz files were found at ${param workflow CECRET { ch_for_dataset = Channel.empty() - ch_for_version = Channel.from("Cecret version", workflow.manifest.version).first() + ch_for_version = Channel.from("Cecret version", workflow.manifest.version).collect() ch_prealigned = Channel.empty() ch_versions = Channel.empty() From 199cf7c881185a0f89be9bf4949e9679c35928e0 Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 15:43:08 -0600 Subject: [PATCH 04/17] adjusted version --- modules/artic.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/artic.nf b/modules/artic.nf index c439218..632a84a 100644 --- a/modules/artic.nf +++ b/modules/artic.nf @@ -35,7 +35,7 @@ process artic { # time stamp + capturing tool versions date > \$log artic --version >> \$log - artic_version=\$(artic --version) + artic_version=\$(artic --version | awk '{print \$NF}') cp ${reference} schema/cecret/V1/cecret.reference.fasta cp ${bed} schema/cecret/V1/cecret.scheme.bed From a2d13491662443fe763d3b09d17862b4398b734e Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 15:43:48 -0600 Subject: [PATCH 05/17] adjusted version --- modules/bwa.nf | 2 +- modules/fastp.nf | 4 ++-- modules/ivar.nf | 4 ++-- modules/minimap2.nf | 2 +- modules/seqyclean.nf | 4 ++-- 5 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/bwa.nf b/modules/bwa.nf index 38062d3..c62711a 100644 --- a/modules/bwa.nf +++ b/modules/bwa.nf @@ -34,7 +34,7 @@ process bwa { # time stamp + capturing tool versions date > \$log echo "bwa \$(bwa 2>&1 | grep Version )" >> \$log - bwa_version="bwa : "\$(bwa 2>&1 | grep Version) + bwa_version=\$(bwa 2>&1 | grep Version | awk '{print \$NF}') # index the reference fasta file bwa index ${reference_genome} diff --git a/modules/fastp.nf b/modules/fastp.nf index ae3a11b..00a3c85 100644 --- a/modules/fastp.nf +++ b/modules/fastp.nf @@ -37,7 +37,7 @@ process fastp { # time stamp + capturing tool versions date > \$log fastp --version >> \$log - cleaner_version="\$(fastp --version 2>&1 | head -n 1)" + cleaner_version=\$(fastp --version 2>&1 | awk '{print \$NF}') fastp ${args} \ -i ${reads[0]} \ @@ -63,7 +63,7 @@ process fastp { # time stamp + capturing tool versions date > \$log fastp --version >> \$log - cleaner_version="\$(fastp --version 2>&1 | head -n 1)" + cleaner_version=\$(fastp --version 2>&1 | awk '{print \$NF}') fastp ${args} \ -i ${reads} \ diff --git a/modules/ivar.nf b/modules/ivar.nf index 1429a97..ed433b8 100644 --- a/modules/ivar.nf +++ b/modules/ivar.nf @@ -36,7 +36,7 @@ process ivar_consensus { date > \$log samtools --version >> \$log ivar version >> \$log - ivar_version=\$(ivar version | grep "version") + ivar_version=\$(ivar version | head -n 1 | awk '{print \$NF}') samtools mpileup -A -d ${params.mpileup_depth} -B -Q 0 --reference ${reference_genome} ${bam} | \ ivar consensus ${args} -m ${params.minimum_depth} -p ivar_consensus/${prefix}.consensus | tee -a \$log @@ -160,7 +160,7 @@ process ivar_trim { # time stamp + capturing tool versions date > \$log ivar version >> \$log - trimmer_version="ivar : \$(ivar version | grep version)" + trimmer_version=\$(ivar version | head -n 1 | awk '{print \$NF}') # trimming the reads ivar trim ${args} -e -i ${bam} -b ${primer_bed} -p ivar_trim/${prefix}.primertrim | tee -a \$log diff --git a/modules/minimap2.nf b/modules/minimap2.nf index 259c904..3d6ac55 100644 --- a/modules/minimap2.nf +++ b/modules/minimap2.nf @@ -34,7 +34,7 @@ process minimap2 { # time stamp + capturing tool versions date > \$log minimap2 --version >> \$log - minimap2_version=\$(echo "minimap2 : "\$(minimap2 --version)) + minimap2_version=\$(minimap2 --version | awk '{print \$NF}') minimap2 ${args} \ -ax sr -t ${task.cpus} \ diff --git a/modules/seqyclean.nf b/modules/seqyclean.nf index 1bd1434..6ba58fd 100644 --- a/modules/seqyclean.nf +++ b/modules/seqyclean.nf @@ -36,7 +36,7 @@ process seqyclean { # time stamp + capturing tool versions date > \$log echo "seqyclean version: \$(seqyclean -h | grep Version)" >> \$log - cleaner_version="seqyclean : \$(seqyclean -h | grep Version)" + cleaner_version=\$(seqyclean -h | grep Version | head -n 1 | awk '{print \$2 "_" \$3}' ) seqyclean ${args} \ -c ${params.seqyclean_contaminant_file} \ @@ -59,7 +59,7 @@ process seqyclean { # time stamp + capturing tool versions date > \$log echo "seqyclean version: \$(seqyclean -h | grep Version)" >> \$log - cleaner_version="seqyclean : \$(seqyclean -h | grep Version)" + cleaner_version=\$(seqyclean -h | grep Version | head -n 1 | awk '{print \$2 "_" \$3}' ) seqyclean ${args} \ -c ${params.seqyclean_contaminant_file} \ From 4452fbf3e80c13ca3e16312395e7615e8c870197 Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 15:44:09 -0600 Subject: [PATCH 06/17] adding result files to summary --- subworkflows/mpx.nf | 2 +- subworkflows/sarscov2.nf | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/mpx.nf b/subworkflows/mpx.nf index cd144f7..d2766d0 100644 --- a/subworkflows/mpx.nf +++ b/subworkflows/mpx.nf @@ -26,7 +26,7 @@ workflow mpx { emit: for_multiqc = nextclade.out.nextclade_file - for_summary = vadr.out.vadr_file + for_summary = vadr.out.vadr_file.mix(nextclade.out.nextclade_file) prealigned = nextclade.out.prealigned dataset = ch_dataset versions = ch_versions diff --git a/subworkflows/sarscov2.nf b/subworkflows/sarscov2.nf index 566d6a5..4b4b639 100644 --- a/subworkflows/sarscov2.nf +++ b/subworkflows/sarscov2.nf @@ -50,6 +50,6 @@ workflow sarscov2 { dataset = ch_dataset prealigned = nextclade.out.prealigned for_multiqc = pangolin.out.pangolin_file.mix(nextclade.out.nextclade_file).mix(freyja_aggregate.out.for_multiqc) - for_summary = freyja_aggregate.out.aggregated_freyja_file.mix(vadr.out.vadr_file).mix(pango_collapse.out.results) + for_summary = freyja_aggregate.out.aggregated_freyja_file.mix(vadr.out.vadr_file).mix(pango_collapse.out.results).mix(nextclade.out.nextclade_file).mix(pangolin.out.pangolin_file) versions = ch_versions } From c9e130a83adb445b8f408f091f2c5e7fdb77ddbe Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 15:44:22 -0600 Subject: [PATCH 07/17] adjusted version --- modules/samtools.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/samtools.nf b/modules/samtools.nf index 3991cda..31004c0 100644 --- a/modules/samtools.nf +++ b/modules/samtools.nf @@ -405,7 +405,7 @@ process samtools_ampliconclip { # time stamp + capturing tool versions date > \$log samtools --version >> \$log - trimmer_version="samtools ampliconclip : \$(samtools --version | head -n 1)" + trimmer_version=\$(samtools --version | head -n 1 | awk '{print \$NF}') # trimming the reads samtools ampliconclip ${args} -b ${primer_bed} ${bam} | \ From 9c57fcc3ebc3ab65856389c2a10f32656bacca08 Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 15:44:40 -0600 Subject: [PATCH 08/17] reformated --- nextflow_schema.json | 1212 ++++++++++++++++++++++-------------------- 1 file changed, 634 insertions(+), 578 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 31cf9ab..0aabb13 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -4,584 +4,640 @@ "title": "Cecret Parameters", "description": "Cecret is a workflow for reference-based sequencing of organisms with small genomes, such as SARS-CoV-2", "type": "object", - "properties": { - "aci": { - "type": "boolean", - "description": "Specifies if process should be used", - "hidden": true, - "default": true - }, - "aligner": { - "type": "string", - "description": "Specifies which aligner is going to be used.", - "hidden": true, - "default": "bwa", - "enum": [ - "bwa", - "minimap2" - ] - }, - "amplicon_bed": { - "type": "string", - "hidden": true, - "description": "Bedfile for amplicons" - }, - "artic_options": { - "type": "string", - "description": "Options for process", - "hidden": true, - "default": "--normalise 200 --skip-nanopolish --medaka --medaka-model r941_min_high_g360" - }, - "artic_read_filtering_options": { - "type": "string", - "description": "Options for process", - "hidden": true, - "default": "--min-length 400 --max-length 700" - }, - "bbnorm": { - "type": "boolean", - "hidden": true, - "default": false, - "description": "Specifies if process should be used" - }, - "bbnorm_options": { - "type": "string", - "hidden": true, - "default": "target=200 min=5", - "description": "Options for process" - }, - "bcftools_variants": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "bcftools_variants_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "cleaner": { - "type": "string", - "hidden": true, - "default": "seqyclean", - "description": "Specifies what tool to use to remove low quality reads", - "enum": [ - "seqyclean", - "fastp" - ] - }, - "config_file": { - "type": "boolean", - "hidden": true, - "default": false, - "description" : "Specifies if a config file is copied for the end user. Ends script." - }, - "download_nextclade_dataset": { - "type": "boolean", - "hidden": false, - "description" : "Specifies if nextclade should download its dataset. Set to false to use included dataset.", - "default" : false - }, - "fastas": { - "type": "string", - "description": "input channel for fastas" - }, - "fastp_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "fastqc": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "fastqc_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "filter": { - "type": "boolean", - "hidden": true, - "default": false, - "description": "Specifies if process should be used" - }, - "filter_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "freyja": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "freyja_aggregate": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "freyja_aggregate_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "freyja_demix_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "freyja_plot_filetype": { - "type": "string", - "hidden": true, - "default": "png", - "description": "Specifies filetype for freyja plot", - "enum": [ - ".pdf", - ".png" - ] - }, - "freyja_plot_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "freyja_variants_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "gff": { - "type": "string", - "hidden": true, - "description": "File used in ivar variants. Must correspond with reference genome." - }, - "heatcluster": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "heatcluster_options": { - "type": "string", - "hidden": true, - "default": "-t png", - "description": "Options for process" - }, - "igv_reports": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "igv_reports_options": { - "type": "string", - "hidden": true, - "default": "--flanking 1000", - "description": "Options for process" - }, - "iqtree2": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "iqtree2_options": { - "type": "string", - "hidden": true, - "default": "-ninit 2 -n 2 -me 0.05 -m GTR", - "description": "Options for process" - }, - "iqtree2_outgroup": { - "type": "string", - "hidden": true, - "default": "MN908947", - "description": "outgroup for multiple sequence alignment" - }, - "ivar_consensus_options": { - "type": "string", - "hidden": true, - "default": "-q 20 -t 0.6 -n N", - "description": "Options for process" - }, - "ivar_trim_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "ivar_variants": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "ivar_variants_options": { - "type": "string", - "hidden": true, - "default": "-q 20 -t 0.6", - "description": "Options for process" - }, - "kraken2": { - "type": "boolean", - "default": false, - "description": "Specifies if process should be used" - }, - "kraken2_db": { - "type": "string", - "default": "false", - "description": "directory to kraken2 database" - }, - "kraken2_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "mafft_options": { - "type": "string", - "hidden": true, - "default": "--maxambiguous 0.5", - "description": "Options for process" - }, - "markdup": { - "type": "boolean", - "hidden": true, - "default": false, - "description": "Deduplication toggle" - }, - "maxcpus": { - "type": "string", - "hidden": true, - "default": 8, - "description": "maximum number of cpus per process" - }, - "medcpus": { - "type": "string", - "hidden": true, - "default": 4, - "description": "medium amount of cpus for some processes" - }, - "minimap2_options": { - "type": "string", - "hidden": true, - "default": "-K 20M", - "description": "Options for process" - }, - "minimum_depth": { - "type": "number", - "hidden": true, - "default": 100, - "description": "minimum depth for calling a variant" - }, - "mpileup_depth": { - "type": "number", - "hidden": true, - "default": 8000, - "description": "number of reads put into memory by samtools/bcftools" - }, - "msa": { - "type": "string", - "hidden": true, - "default": "mafft", - "description": "Specifies what tool to use for multiple sequence alignment. Current options are nextclade and mafft.", - "enum": [ - "nextclade", - "mafft" - ] - }, - "multifastas": { - "type": "string", - "description": "input channel for multifasta files" - }, - "multiqc": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "multiqc_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "nanopore": { - "type": "string", - "hidden": true, - "description": "Directory with nanopore fastq files" - }, - "nextclade": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "nextclade_dataset": { - "type": "string", - "hidden": true, - "default": "sars-cov-2", - "description": "Specifies nextclade dataset" - }, - "nextclade_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "outdir": { - "type": "string", - "default": "cecret", - "description": "Specifies where results are saved" - }, - "pango_collapse":{ - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "pango_collapse_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "pangolin": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "pangolin_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "phytreeviz": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "phytreeviz_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "predownloaded_nextclade_dataset": { - "type": "string", - "hidden": true, - "description": "Specifies a zipped nextclade dataset to use instead of downloading during runtime." - }, - "primer_bed": { - "type": "string", - "hidden": true, - "description": "File with bedfile of primers used in the analysis" - }, - "primer_set": { - "type": "string", - "hidden": true, - "default": "ncov_V4", - "description": "Specifies a primer set included in repo", - "enum": [ - "midnight_idt_V1", - "midnight_ont_V1", - "midnight_ont_V2", - "midnight_ont_V3", - "ncov_V3", - "ncov_V4", - "ncov_V4.1", - "ncov_V5.3.2", - "mpx_primalseq", - "mpx_idt" - ] - }, - "reads": { - "type": "string", - "hidden": true, - "description": "Directory with paired-end fastq files" - }, - "reference_genome": { - "type": "string", - "hidden": true, - "description": "THE Reference genome" - }, - "relatedness": { - "type": "boolean", - "default": false, - "description": "Specifies if subworkflow should be used" - }, - "sample_sheet": { - "type": "string", - "description": "sample sheet with sample, fastq_1, and fastq_2 columns" - }, - "samtools_ampliconclip_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "samtools_ampliconstats": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "samtools_ampliconstats_options": { - "type": "string", - "hidden": true, - "default": "--max-amplicon-length 3000 --max-amplicons 3000", - "description": "Options for process" - }, - "samtools_coverage": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "samtools_coverage_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "samtools_depth": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "samtools_depth_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "samtools_fixmate_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "samtools_flagstat": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "samtools_flagstat_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "samtools_markdup_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "samtools_plot_ampliconstats": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "samtools_plot_ampliconstats_options": { - "type": "string", - "hidden": true, - "default": "-size 1200,900 -size2 1200,900 -size3 1200,900", - "description": "Options for process" - }, - "samtools_stats": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "samtools_stats_options": { - "type": "string", - "hidden": true, - "description": "Options for process" - }, - "seqyclean_contaminant_file": { - "type": "string", - "hidden": true, - "default": "/Adapters_plus_PhiX_174.fasta", - "description": "Specifies contaminant file in seqyclean container" - }, - "seqyclean_options": { - "type": "string", - "hidden": true, - "default": "-minlen 25 -qual", - "description": "Options for process" - }, - "single_reads": { - "type": "string", - "description": "Specifies directory for single reads" - }, - "snpdists": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "snpdists_options": { - "type": "string", - "hidden": true, - "default": "-c", - "description": "Options for process" - }, - "species": { - "type": "string", - "default": "sarscov2", - "description": "specifies SARS-CoV-2 or MPX options", - "enum": [ - "other", - "mpx", - "sarscov2" - ] - }, - "sra_accessions":{ - "type": "string", - "hidden": true, - "default": [], - "description": "list of sra acessions to download with wget from ENA" - }, - "trimmer": { - "type": "string", - "hidden": true, - "default": "ivar", - "description": "Specifies which tool to use to trim primers from primerbedfile", - "enum": [ - "samtools", - "ivar", - "none" - ] - }, - "vadr": { - "type": "boolean", - "hidden": true, - "default": true, - "description": "Specifies if process should be used" - }, - "vadr_mdir": { - "type": "string", - "hidden": true, - "default": "/opt/vadr/vadr-models", - "description": "Specifies model directory in container" - }, - "vadr_options": { - "type": "string", - "hidden": true, - "default": "--split --glsearch -s -r --nomisc --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn", - "description": "Options for process" + "definitions":{ + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "required": [ + "sample_sheet", + "outdir" + ], + "properties": { + "amplicon_bed": { + "type": "string", + "hidden": true, + "description": "Bedfile for amplicons" + }, + "fastas": { + "type": "string", + "description": "input channel for fastas" + }, + "gff": { + "type": "string", + "hidden": true, + "description": "File used in ivar variants. Must correspond with reference genome." + }, + "kraken2_db": { + "type": "string", + "default": "false", + "description": "directory to kraken2 database" + }, + "multifastas": { + "type": "string", + "description": "input channel for multifasta files" + }, + "nanopore": { + "type": "string", + "hidden": true, + "description": "Directory with nanopore fastq files" + }, + "outdir": { + "type": "string", + "default": "cecret", + "description": "Specifies where results are saved" + }, + "predownloaded_nextclade_dataset": { + "type": "string", + "hidden": true, + "description": "Specifies a zipped nextclade dataset to use instead of downloading during runtime." + }, + "primer_bed": { + "type": "string", + "hidden": true, + "description": "File with bedfile of primers used in the analysis" + }, + "reads": { + "type": "string", + "hidden": true, + "description": "Directory with paired-end fastq files" + }, + "reference_genome": { + "type": "string", + "hidden": true, + "description": "THE Reference genome" + }, + "sample_sheet": { + "type": "string", + "description": "sample sheet with sample, fastq_1, and fastq_2 columns" + } + } + }, + "pipeline_configuration_options": { + "title": "Pipeline Configuration options", + "type": "object", + "description": "Options to configure how the workflow runs.", + "properties": { + "aci": { + "type": "boolean", + "description": "Specifies if process should be used", + "hidden": true, + "default": true + }, + "aligner": { + "type": "string", + "description": "Specifies which aligner is going to be used.", + "hidden": true, + "default": "bwa", + "enum": [ + "bwa", + "minimap2" + ] + }, + "artic_options": { + "type": "string", + "description": "Options for process", + "hidden": true, + "default": "--normalise 200 --skip-nanopolish --medaka --medaka-model r941_min_high_g360" + }, + "artic_read_filtering_options": { + "type": "string", + "description": "Options for process", + "hidden": true, + "default": "--min-length 400 --max-length 700" + }, + "bbnorm": { + "type": "boolean", + "hidden": true, + "default": false, + "description": "Specifies if process should be used" + }, + "bbnorm_options": { + "type": "string", + "hidden": true, + "default": "target=200 min=5", + "description": "Options for process" + }, + "bcftools_variants": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "bcftools_variants_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "cleaner": { + "type": "string", + "hidden": true, + "default": "seqyclean", + "description": "Specifies what tool to use to remove low quality reads", + "enum": [ + "seqyclean", + "fastp" + ] + }, + "download_nextclade_dataset": { + "type": "boolean", + "hidden": false, + "description" : "Specifies if nextclade should download its dataset. Set to false to use included dataset.", + "default" : false + }, + "fastp_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "fastqc": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "fastqc_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "filter": { + "type": "boolean", + "hidden": true, + "default": false, + "description": "Specifies if process should be used" + }, + "filter_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "freyja": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "freyja_aggregate": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "freyja_aggregate_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "freyja_demix_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "freyja_plot_filetype": { + "type": "string", + "hidden": true, + "default": "png", + "description": "Specifies filetype for freyja plot", + "enum": [ + ".pdf", + ".png" + ] + }, + "freyja_plot_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "freyja_variants_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "heatcluster": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "heatcluster_options": { + "type": "string", + "hidden": true, + "default": "-t png", + "description": "Options for process" + }, + "igv_reports": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "igv_reports_options": { + "type": "string", + "hidden": true, + "default": "--flanking 1000", + "description": "Options for process" + }, + "iqtree2": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "iqtree2_options": { + "type": "string", + "hidden": true, + "default": "-ninit 2 -n 2 -me 0.05 -m GTR", + "description": "Options for process" + }, + "iqtree2_outgroup": { + "type": "string", + "hidden": true, + "default": "MN908947", + "description": "outgroup for multiple sequence alignment" + }, + "ivar_consensus_options": { + "type": "string", + "hidden": true, + "default": "-q 20 -t 0.6 -n N", + "description": "Options for process" + }, + "ivar_trim_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "ivar_variants": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "ivar_variants_options": { + "type": "string", + "hidden": true, + "default": "-q 20 -t 0.6", + "description": "Options for process" + }, + "kraken2": { + "type": "boolean", + "default": false, + "description": "Specifies if process should be used" + }, + "kraken2_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "mafft_options": { + "type": "string", + "hidden": true, + "default": "--maxambiguous 0.5", + "description": "Options for process" + }, + "markdup": { + "type": "boolean", + "hidden": true, + "default": false, + "description": "Deduplication toggle" + }, + "maxcpus": { + "type": "string", + "hidden": true, + "default": 8, + "description": "maximum number of cpus per process" + }, + "medcpus": { + "type": "string", + "hidden": true, + "default": 4, + "description": "medium amount of cpus for some processes" + }, + "minimap2_options": { + "type": "string", + "hidden": true, + "default": "-K 20M", + "description": "Options for process" + }, + "minimum_depth": { + "type": "number", + "hidden": true, + "default": 100, + "description": "minimum depth for calling a variant" + }, + "mpileup_depth": { + "type": "number", + "hidden": true, + "default": 8000, + "description": "number of reads put into memory by samtools/bcftools" + }, + "msa": { + "type": "string", + "hidden": true, + "default": "mafft", + "description": "Specifies what tool to use for multiple sequence alignment. Current options are nextclade and mafft.", + "enum": [ + "nextclade", + "mafft" + ] + }, + "multiqc": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "multiqc_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "nextclade": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "nextclade_dataset": { + "type": "string", + "hidden": true, + "default": "sars-cov-2", + "description": "Specifies nextclade dataset" + }, + "nextclade_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "pango_collapse":{ + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "pango_collapse_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "pangolin": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "pangolin_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "phytreeviz": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "phytreeviz_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "primer_set": { + "type": "string", + "hidden": true, + "default": "ncov_V4", + "description": "Specifies a primer set included in repo", + "enum": [ + "midnight_idt_V1", + "midnight_ont_V1", + "midnight_ont_V2", + "midnight_ont_V3", + "ncov_V3", + "ncov_V4", + "ncov_V4.1", + "ncov_V5.3.2", + "mpx_primalseq", + "mpx_idt" + ] + }, + "relatedness": { + "type": "boolean", + "default": false, + "description": "Specifies if subworkflow should be used" + }, + "samtools_ampliconclip_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "samtools_ampliconstats": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "samtools_ampliconstats_options": { + "type": "string", + "hidden": true, + "default": "--max-amplicon-length 3000 --max-amplicons 3000", + "description": "Options for process" + }, + "samtools_coverage": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "samtools_coverage_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "samtools_depth": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "samtools_depth_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "samtools_fixmate_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "samtools_flagstat": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "samtools_flagstat_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "samtools_markdup_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "samtools_plot_ampliconstats": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "samtools_plot_ampliconstats_options": { + "type": "string", + "hidden": true, + "default": "-size 1200,900 -size2 1200,900 -size3 1200,900", + "description": "Options for process" + }, + "samtools_stats": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "samtools_stats_options": { + "type": "string", + "hidden": true, + "description": "Options for process" + }, + "seqyclean_contaminant_file": { + "type": "string", + "hidden": true, + "default": "/Adapters_plus_PhiX_174.fasta", + "description": "Specifies contaminant file in seqyclean container" + }, + "seqyclean_options": { + "type": "string", + "hidden": true, + "default": "-minlen 25 -qual", + "description": "Options for process" + }, + "single_reads": { + "type": "string", + "description": "Specifies directory for single reads" + }, + "snpdists": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "snpdists_options": { + "type": "string", + "hidden": true, + "default": "-c", + "description": "Options for process" + }, + "species": { + "type": "string", + "default": "sarscov2", + "description": "specifies SARS-CoV-2 or MPX options", + "enum": [ + "other", + "mpx", + "sarscov2" + ] + }, + "sra_accessions":{ + "type": "string", + "hidden": true, + "default": [], + "description": "list of sra acessions to download with wget from ENA" + }, + "trimmer": { + "type": "string", + "hidden": true, + "default": "ivar", + "description": "Specifies which tool to use to trim primers from primerbedfile", + "enum": [ + "samtools", + "ivar", + "none" + ] + }, + "vadr": { + "type": "boolean", + "hidden": true, + "default": true, + "description": "Specifies if process should be used" + }, + "vadr_mdir": { + "type": "string", + "hidden": true, + "default": "/opt/vadr/vadr-models", + "description": "Specifies model directory in container" + }, + "vadr_options": { + "type": "string", + "hidden": true, + "default": "--split --glsearch -s -r --nomisc --lowsim5seq 6 --lowsim3seq 6 --alt_fail lowscore,insertnn,deletinn", + "description": "Options for process" + }, + "vadr_reference": { + "type": "string", + "hidden": true, + "default": "sarscov2", + "description": "Specifies reference for vadr in container" + }, + "vadr_trim_options": { + "type": "string", + "default": "--minlen 50 --maxlen 30000", + "hidden": true, + "description": "Options for process" + } + } + }, + "generic_options": { + "title": "Generic options", + "type": "object", + "fa_icon": "fas fa-file-import", + "description": "Less common options for the pipeline, typically set in a config file.", + "help_text": "These options are common to all nf-core pipelines and allow you to customize some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", + "properties": { + "config_file": { + "type": "boolean", + "description" : "Specifies if a config file is copied for the end user. Ends script.", + "hidden" : true, + "default" : false + } + } + } + }, + "allOf": [ + { + "$ref": "#/definitions/input_output_options" }, - "vadr_reference": { - "type": "string", - "hidden": true, - "default": "sarscov2", - "description": "Specifies reference for vadr in container" + { + "$ref": "#/definitions/pipeline_configuration_options" }, - "vadr_trim_options": { - "type": "string", - "default": "--minlen 50 --maxlen 30000", - "hidden": true, - "description": "Options for process" + { + "$ref": "#/definitions/generic_options" } - } -} \ No newline at end of file + ] +} + + + + + + + + + + + + + + + + + \ No newline at end of file From 5ac67c17fdda052306a433a399b2ebd82ec6fe28 Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 15:45:15 -0600 Subject: [PATCH 09/17] update to version 3.8.0 --- modules/nextclade.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nextclade.nf b/modules/nextclade.nf index d3a6603..2d74223 100644 --- a/modules/nextclade.nf +++ b/modules/nextclade.nf @@ -2,7 +2,7 @@ process nextclade_dataset { tag "Downloading Dataset" label "process_medium" publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'nextstrain/nextclade:3.7.4' + container 'nextstrain/nextclade:3.8.0' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} @@ -47,7 +47,7 @@ process nextclade { tag "Clade Determination" label "process_medium" publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'nextstrain/nextclade:3.7.4' + container 'nextstrain/nextclade:3.8.0' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 7ff07e0e7fcaae8c98a91a851e9ea9dbdbed4af9 Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 16:05:47 -0600 Subject: [PATCH 10/17] added link --- .github/workflows/github_actions.config | 132 +++++++++++++++++++++++- 1 file changed, 129 insertions(+), 3 deletions(-) diff --git a/.github/workflows/github_actions.config b/.github/workflows/github_actions.config index d5ec949..d3f4dac 100644 --- a/.github/workflows/github_actions.config +++ b/.github/workflows/github_actions.config @@ -1,7 +1,133 @@ -params.vadr = false - process { - withName:ivar_consensus{ + withName:aci{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:artic{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:artic_read_filtering{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:bbnorm{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:bcftools_variants{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:bwa{ + publishDir = [ path: "cecret", mode: 'link', pattern: 'logs/*/*log' ] + } + withName:download{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:fasta_prep{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:summary{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:unzip{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:fastp{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:fastqc{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:freyja_variants{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:freyja_demix{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:freyja_aggregate{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:heatcluster{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:igv_reports{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:iqtree2{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:ivar_consensus{ memory = '4 GB' + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:ivar_variants{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:ivar_trim{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:kraken2{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:mafft{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:minimap2{ + publishDir = [ path: "cecret", mode: 'link', pattern: 'logs/*/*log' ] + } + withName:multiqc_combine{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:nextclade_dataset{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:nextclade{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:pango_collapse{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:pangolin{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:phytreeviz{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_stats{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_coverage{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_flagstat{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_depth{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_ampliconstats{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_plot_ampliconstats{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_sort{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_filter{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_ampliconclip{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:samtools_markdup{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:seqyclean{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:snpdists{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } + withName:vadr{ + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] } } + From 113ba023e2fa2e4cbc29d08db95f2091562cfbff Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 16:06:12 -0600 Subject: [PATCH 11/17] check for kraken2 files --- .github/workflows/test_kraken2.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/test_kraken2.yml b/.github/workflows/test_kraken2.yml index c2ef185..6dbd863 100755 --- a/.github/workflows/test_kraken2.yml +++ b/.github/workflows/test_kraken2.yml @@ -41,5 +41,9 @@ jobs: cat cecret*/cecret_results.txt + - name: Kraken2 results + run: | + wc -l cecret/kraken2/*_kraken2_report.txt + - name: Clean run: rm -rf work .nextflow* \ No newline at end of file From 839fd5f283c7a9f7078eecccadc44d636c94a0bf Mon Sep 17 00:00:00 2001 From: eriny Date: Wed, 3 Jul 2024 16:06:25 -0600 Subject: [PATCH 12/17] added vadr --- .github/workflows/test_mpx_yale.yml | 37 +++++++++++++++++++++++++++++ .github/workflows/test_primers.yml | 3 ++- .github/workflows/test_profile.yml | 2 +- .github/workflows/test_profile1.yml | 2 +- .github/workflows/test_profile2.yml | 2 +- 5 files changed, 42 insertions(+), 4 deletions(-) create mode 100755 .github/workflows/test_mpx_yale.yml diff --git a/.github/workflows/test_mpx_yale.yml b/.github/workflows/test_mpx_yale.yml new file mode 100755 index 0000000..6862940 --- /dev/null +++ b/.github/workflows/test_mpx_yale.yml @@ -0,0 +1,37 @@ +name: Test mpx workflow with yale primers + +on: [pull_request, workflow_dispatch] + +run-name: mpx_yale + +jobs: + + test: + runs-on: ubuntu-20.04 + steps: + - name: Checkout + uses: actions/checkout@master + + - name: Install Nextflow + run: | + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ + + - name: Download reads + run: | + mkdir reads + cd reads + wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/024/SRR20689724/SRR20689724_1.fastq.gz + wget -q ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR206/024/SRR20689724/SRR20689724_2.fastq.gz + cd ../ + + - name: Run Cecret + run: | + nextflow run . -profile docker,mpx_yale -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 + + ls cecret* + + head cecret*/cecret_results.txt + + - name: Clean + run: rm -rf work .nextflow* diff --git a/.github/workflows/test_primers.yml b/.github/workflows/test_primers.yml index 6660bd4..4f58283 100644 --- a/.github/workflows/test_primers.yml +++ b/.github/workflows/test_primers.yml @@ -18,7 +18,8 @@ jobs: 'ncov_V3', 'ncov_V4', 'ncov_V4.1', - 'ncov_V5.3.2' + 'ncov_V5.3.2', + 'mpx_yale' ] steps: diff --git a/.github/workflows/test_profile.yml b/.github/workflows/test_profile.yml index 0c5cf10..e68519b 100644 --- a/.github/workflows/test_profile.yml +++ b/.github/workflows/test_profile.yml @@ -24,7 +24,7 @@ jobs: - name: Run Cecret run: | - nextflow run . -profile docker,test -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false + nextflow run . -profile docker,test -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 ls cecret* diff --git a/.github/workflows/test_profile1.yml b/.github/workflows/test_profile1.yml index 57cdcc6..4ff44aa 100644 --- a/.github/workflows/test_profile1.yml +++ b/.github/workflows/test_profile1.yml @@ -24,7 +24,7 @@ jobs: - name: Run Cecret run: | - nextflow run . -profile docker,test1 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false + nextflow run . -profile docker,test1 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 ls cecret* diff --git a/.github/workflows/test_profile2.yml b/.github/workflows/test_profile2.yml index 4f681ff..4735f3a 100644 --- a/.github/workflows/test_profile2.yml +++ b/.github/workflows/test_profile2.yml @@ -24,7 +24,7 @@ jobs: - name: Run Cecret run: | - nextflow run . -profile docker,test2 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 --vadr false + nextflow run . -profile docker,test2 -c .github/workflows/github_actions.config --maxcpus 2 --medcpus 2 --cleaner 'fastp' --aligner 'minimap2' --mpileup_depth 200 ls cecret* From 55e756237cebc35986d766aeb7286485daaebcfb Mon Sep 17 00:00:00 2001 From: Young Date: Wed, 3 Jul 2024 16:38:24 -0600 Subject: [PATCH 13/17] added ignore to errorStrategy --- .github/workflows/github_actions.config | 175 ++++++++++++------------ 1 file changed, 88 insertions(+), 87 deletions(-) diff --git a/.github/workflows/github_actions.config b/.github/workflows/github_actions.config index d3f4dac..f41502f 100644 --- a/.github/workflows/github_actions.config +++ b/.github/workflows/github_actions.config @@ -1,133 +1,134 @@ process { + errorStrategy = { task.attempt < 2 ? 'retry' : 'terminate'} withName:aci{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:artic{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:artic_read_filtering{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:bbnorm{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:bcftools_variants{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:bwa{ - publishDir = [ path: "cecret", mode: 'link', pattern: 'logs/*/*log' ] - } + publishDir = [ path: "cecret", mode: 'link', pattern: 'logs/*/*log' ] + } withName:download{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:fasta_prep{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:summary{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:unzip{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:fastp{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:fastqc{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:freyja_variants{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:freyja_demix{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:freyja_aggregate{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:heatcluster{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:igv_reports{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:iqtree2{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:ivar_consensus{ - memory = '4 GB' - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + memory = '4 GB' + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:ivar_variants{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:ivar_trim{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:kraken2{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:mafft{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:minimap2{ - publishDir = [ path: "cecret", mode: 'link', pattern: 'logs/*/*log' ] - } + publishDir = [ path: "cecret", mode: 'link', pattern: 'logs/*/*log' ] + } withName:multiqc_combine{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:nextclade_dataset{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:nextclade{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:pango_collapse{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:pangolin{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:phytreeviz{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_stats{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_coverage{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_flagstat{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_depth{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_ampliconstats{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_plot_ampliconstats{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_sort{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_filter{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_ampliconclip{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:samtools_markdup{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:seqyclean{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:snpdists{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } withName:vadr{ - publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] - } + publishDir = [ path: "cecret", mode: 'link', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }] + } } From f51b59b5975217b22268b4c7e7d55650dbe5efd9 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 9 Jul 2024 14:11:51 -0600 Subject: [PATCH 14/17] Update freyja to 1.5.1-07_02_2024-01-27-2024-07-09 --- modules/freyja.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/freyja.nf b/modules/freyja.nf index 525f044..85473f9 100644 --- a/modules/freyja.nf +++ b/modules/freyja.nf @@ -3,7 +3,7 @@ process freyja_variants { label "process_medium" //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/freyja:1.5.1' + container 'staphb/freyja:1.5.1-07_02_2024-01-27-2024-07-09' //#UPHLICA maxForks 10 //#UPHLICA pod annotation: 'scheduler.illumina.com/presetSize', value: 'standard-xlarge' @@ -53,7 +53,7 @@ process freyja_demix { label "process_medium" //errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/freyja:1.5.1' + container 'staphb/freyja:1.5.1-07_02_2024-01-27-2024-07-09' //#UPHLICA maxForks 10 @@ -105,7 +105,7 @@ process freyja_aggregate { tag "Aggregating results from freyja" label "process_single" publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/freyja:1.5.1' + container 'staphb/freyja:1.5.1-07_02_2024-01-27-2024-07-09' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 4a9dce6a7e6fac69d5dab46f27ddcd948017fef7 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 9 Jul 2024 14:13:41 -0600 Subject: [PATCH 15/17] add docker rmi --- .github/workflows/check_versions.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/check_versions.yml b/.github/workflows/check_versions.yml index 2c268e2..a979bd1 100644 --- a/.github/workflows/check_versions.yml +++ b/.github/workflows/check_versions.yml @@ -36,6 +36,8 @@ jobs: echo "New version for $base! Upgrade to $latest_version from $workflow_version." | tee -a versions.txt issue_text="$issue_text
- $base from $workflow_version to $latest_version " fi + + docker rmi $base:latest done latest_nextclade_version=$(docker run nextstrain/nextclade:latest nextclade --version | awk '{print $2}') From 54a1db657c8624a5e74b2fadf0341fa8557482d1 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 9 Jul 2024 14:14:28 -0600 Subject: [PATCH 16/17] Update pangolin to 4.3.1-pdata-1.28.1 --- modules/pangolin.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/pangolin.nf b/modules/pangolin.nf index 32a62a7..2386e8b 100644 --- a/modules/pangolin.nf +++ b/modules/pangolin.nf @@ -2,7 +2,7 @@ process pangolin { tag "SARS-CoV-2 lineage Determination" label "process_medium" publishDir path: params.outdir, mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - container 'staphb/pangolin:4.3.1-pdata-1.28' + container 'staphb/pangolin:4.3.1-pdata-1.28.1' //#UPHLICA maxForks 10 //#UPHLICA errorStrategy { task.attempt < 2 ? 'retry' : 'ignore'} From 5be5d8ca517662c5e9c976a76fb99ebf1460ec1a Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 9 Jul 2024 14:14:45 -0600 Subject: [PATCH 17/17] Update nextflow.config to 3.15.24191 --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index f121b5f..ee37954 100644 --- a/nextflow.config +++ b/nextflow.config @@ -5,7 +5,7 @@ manifest { name = 'Cecret' author = 'Erin Young' homePage = 'https://github.com/UPHL-BioNGS/Cecret' - version = 'v3.15.24184' + version = 'v3.15.24191' defaultBranch = 'master' recurseSubmodules = false description = 'Reference-based consensus creation'