From 6e94fc4469afed9caa7e215fe5a6ad16d5394cce Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Thu, 30 May 2024 11:10:34 +0200 Subject: [PATCH 1/2] reviewer 2 suggestions before v2.3.0 release --- README.md | 3 ++- bin/multiqc_to_custom_csv.py | 2 +- conf/test_full.config | 2 +- docs/output.md | 2 +- nextflow_schema.json | 4 ++-- 5 files changed, 7 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 589004f..ab49676 100644 --- a/README.md +++ b/README.md @@ -50,7 +50,8 @@ In all cases, the assembly is assessed using [QUAST](http://bioinf.spbau.ru/quas If Kmerfinder is invoked, the pipeline will group samples according to the [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/)-estimated reference genomes. Afterwards, two QUAST steps will be carried out: an initial ('general') [QUAST](http://bioinf.spbau.ru/quast) of all samples without reference genomes, and subsequently, a 'by reference genome' [QUAST](http://bioinf.spbau.ru/quast) to aggregate samples with their reference genomes. -> NOTE: This scenario is supported when [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/) analysis is performed only. +> [!NOTE] +> This scenario is supported when [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/) analysis is performed only. ## Usage diff --git a/bin/multiqc_to_custom_csv.py b/bin/multiqc_to_custom_csv.py index 3838ab5..01e3844 100755 --- a/bin/multiqc_to_custom_csv.py +++ b/bin/multiqc_to_custom_csv.py @@ -1,6 +1,6 @@ #!/usr/bin/env python # Sourced and Edited from nf-core/viralrecon: -# https://github.com/nf-core/viralrecon/blob/master/bin/multiqc_to_custom_csv.py#L59 +# https://github.com/nf-core/viralrecon/blob/master/bin/multiqc_to_custom_csv.py import os import sys import errno diff --git a/conf/test_full.config b/conf/test_full.config index 669ae22..f51aa6d 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,7 +15,7 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - input = 'https://raw.githubusercontent.com/nf-core/test-datasets/bacass/bacass_full.tsv' + input = params.pipelines_testdata_base_path + 'bacass/bacass_full.tsv' kraken2db = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard_8gb_20210517.tar.gz' kmerfinderdb = 'https://zenodo.org/records/10458361/files/20190108_kmerfinder_stable_dirs.tar.gz' ncbi_assembly_metadata = 'https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt' diff --git a/docs/output.md b/docs/output.md index 500aa6d..5d0f0da 100644 --- a/docs/output.md +++ b/docs/output.md @@ -255,7 +255,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - `multiqc_plots/`: directory containing static images from the report in various formats. - - summary_assembly_metrics_mqc.csv: custom table containing most relevant assembly QC metrics. + - `summary_assembly_metrics_mqc.csv`: custom table containing most relevant assembly QC metrics. diff --git a/nextflow_schema.json b/nextflow_schema.json index ce8b1a5..8eec000 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -83,7 +83,7 @@ }, "kmerfinderdb": { "type": "string", - "description": "Path to the Kmerfinder bacteria database." + "description": "Path to the Kmerfinder bacteria database. For more details, see [Kmerfinder Databases](https://bitbucket.org/genomicepidemiology/kmerfinder_db/src/master/). You can also download precomputed Kmerfinder database (dated 2019/01/08) from https://zenodo.org/records/10458361/files/20190108_kmerfinder_stable_dirs.tar.gz " }, "reference_fasta": { "type": "string", @@ -215,7 +215,7 @@ }, "skip_kmerfinder": { "type": "boolean", - "description": "Skip contamination analysis with Kmerfinder", + "description": "Skip contamination analysis with [Kmerfinder](https://bitbucket.org/genomicepidemiology/kmerfinder/src/master/)", "fa_icon": "fas fa-forward" }, "skip_annotation": { From cb1c2583f3cca4b76819d125c75accb033a67404 Mon Sep 17 00:00:00 2001 From: Daniel-VM Date: Mon, 3 Jun 2024 08:39:00 +0200 Subject: [PATCH 2/2] add stable url --- bin/multiqc_to_custom_csv.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/bin/multiqc_to_custom_csv.py b/bin/multiqc_to_custom_csv.py index 01e3844..47b7dcc 100755 --- a/bin/multiqc_to_custom_csv.py +++ b/bin/multiqc_to_custom_csv.py @@ -1,6 +1,6 @@ #!/usr/bin/env python # Sourced and Edited from nf-core/viralrecon: -# https://github.com/nf-core/viralrecon/blob/master/bin/multiqc_to_custom_csv.py +# https://github.com/nf-core/viralrecon/blob/3731dd3a32a67a2648ea22c2bd980c224abdaee2/bin/multiqc_to_custom_csv.py import os import sys import errno