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Merge pull request #356 from ENCODE-DCC/WRAN-1863_update_default_geno…
…me_tsv_to_v4 Wran 1863 update default genome tsv to v4
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@@ -7,10 +7,10 @@ struct RuntimeEnvironment { | |
} | ||
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workflow atac { | ||
String pipeline_ver = 'v2.0.3' | ||
String pipeline_ver = 'v2.1.0' | ||
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meta { | ||
version: 'v2.0.3' | ||
version: 'v2.1.0' | ||
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author: 'Jin wook Lee' | ||
email: '[email protected]' | ||
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@@ -19,8 +19,8 @@ workflow atac { | |
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specification_document: 'https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit?usp=sharing' | ||
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default_docker: 'encodedcc/atac-seq-pipeline:v2.0.3' | ||
default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.0.3.sif' | ||
default_docker: 'encodedcc/atac-seq-pipeline:v2.1.0' | ||
default_singularity: 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.1.0.sif' | ||
default_conda: 'encode-atac-seq-pipeline' | ||
croo_out_def: 'https://storage.googleapis.com/encode-pipeline-output-definition/atac.croo.v5.json' | ||
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@@ -72,8 +72,8 @@ workflow atac { | |
} | ||
input { | ||
# group: runtime_environment | ||
String docker = 'encodedcc/atac-seq-pipeline:v2.0.3' | ||
String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.0.3.sif' | ||
String docker = 'encodedcc/atac-seq-pipeline:v2.1.0' | ||
String singularity = 'https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.1.0.sif' | ||
String conda = 'encode-atac-seq-pipeline' | ||
String conda_macs2 = 'encode-atac-seq-pipeline-macs2' | ||
String conda_spp = 'encode-atac-seq-pipeline-spp' | ||
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@@ -1,10 +1,10 @@ | ||
{ | ||
"test_annot_enrich.blacklist" : "atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38.blacklist.bed.gz", | ||
"test_annot_enrich.dnase" : "atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz", | ||
"test_annot_enrich.prom" : "atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz", | ||
"test_annot_enrich.enh" : "atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz", | ||
"test_annot_enrich.blacklist" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38.blacklist.bed.gz", | ||
"test_annot_enrich.dnase" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_all_p10_ucsc.hg19_to_hg38.bed.gz", | ||
"test_annot_enrich.prom" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_prom_p2.hg19_to_hg38.bed.gz", | ||
"test_annot_enrich.enh" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38/ataqc/reg2map_honeybadger2_dnase_enh_p2.hg19_to_hg38.bed.gz", | ||
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"test_annot_enrich.ta" : "atac-seq-pipeline-test-data/input/pe/ataqc/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz", | ||
"test_annot_enrich.ta" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/ataqc/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz", | ||
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"test_annot_enrich.ref_annot_enrich_qc" : "atac-seq-pipeline-test-data/ref_output/test_annot_enrich/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.annot_enrich.qc" | ||
"test_annot_enrich.ref_annot_enrich_qc" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_annot_enrich/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.annot_enrich.qc" | ||
} |
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@@ -1,14 +1,14 @@ | ||
{ | ||
"test_bam2ta.pe_nodup_bam" : "atac-seq-pipeline-test-data/input/pe/nodup_bams/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.bam", | ||
"test_bam2ta.se_nodup_bam" : "atac-seq-pipeline-test-data/input/se/nodup_bams/rep1/ENCFF439VSY.subsampled.400.trim.merged.nodup.bam", | ||
"test_bam2ta.pe_nodup_bam" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/nodup_bams/rep1/ENCFF341MYG.subsampled.400.trim.merged.nodup.bam", | ||
"test_bam2ta.se_nodup_bam" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/nodup_bams/rep1/ENCFF439VSY.subsampled.400.trim.merged.nodup.bam", | ||
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"test_bam2ta.ref_pe_ta" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz", | ||
"test_bam2ta.ref_pe_ta_disable_tn5_shift" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/disable_tn5_shift/ENCFF341MYG.subsampled.400.trim.merged.nodup.tagAlign.gz", | ||
"test_bam2ta.ref_pe_ta_subsample" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/subsample/fix_PIP-917/ENCFF341MYG.subsampled.400.trim.merged.nodup.5K.tn5.tagAlign.gz", | ||
"test_bam2ta.ref_pe_ta" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/ENCFF341MYG.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz", | ||
"test_bam2ta.ref_pe_ta_disable_tn5_shift" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/disable_tn5_shift/ENCFF341MYG.subsampled.400.trim.merged.nodup.tagAlign.gz", | ||
"test_bam2ta.ref_pe_ta_subsample" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/pe/subsample/fix_PIP-917/ENCFF341MYG.subsampled.400.trim.merged.nodup.5K.tn5.tagAlign.gz", | ||
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"test_bam2ta.ref_se_ta" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/ENCFF439VSY.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz", | ||
"test_bam2ta.ref_se_ta_disable_tn5_shift" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/disable_tn5_shift/ENCFF439VSY.subsampled.400.trim.merged.nodup.tagAlign.gz", | ||
"test_bam2ta.ref_se_ta_subsample" : "atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/subsample/ENCFF439VSY.subsampled.400.trim.merged.nodup.5K.tn5.tagAlign.gz", | ||
"test_bam2ta.ref_se_ta" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/ENCFF439VSY.subsampled.400.trim.merged.nodup.tn5.tagAlign.gz", | ||
"test_bam2ta.ref_se_ta_disable_tn5_shift" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/disable_tn5_shift/ENCFF439VSY.subsampled.400.trim.merged.nodup.tagAlign.gz", | ||
"test_bam2ta.ref_se_ta_subsample" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bam2ta/se/subsample/ENCFF439VSY.subsampled.400.trim.merged.nodup.5K.tn5.tagAlign.gz", | ||
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"test_bam2ta.bam2ta_subsample" : 5000 | ||
} |
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{ | ||
"test_bowtie2.pe_fastqs_R1" : [ | ||
"atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz", | ||
"atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz" | ||
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/ENCFF341MYG.subsampled.400.fastq.gz", | ||
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair1/ENCFF106QGY.subsampled.400.fastq.gz" | ||
], | ||
"test_bowtie2.pe_fastqs_R2" : [ | ||
"atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz", | ||
"atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz" | ||
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/ENCFF248EJF.subsampled.400.fastq.gz", | ||
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/pe/fastqs/rep1/pair2/ENCFF368TYI.subsampled.400.fastq.gz" | ||
], | ||
"test_bowtie2.se_fastqs_R1" : [ | ||
"atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF439VSY.subsampled.400.fastq.gz", | ||
"atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF325FCQ.subsampled.400.fastq.gz", | ||
"atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF683IQS.subsampled.400.fastq.gz", | ||
"atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF744CHW.subsampled.400.fastq.gz" | ||
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF439VSY.subsampled.400.fastq.gz", | ||
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF325FCQ.subsampled.400.fastq.gz", | ||
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF683IQS.subsampled.400.fastq.gz", | ||
"gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/input/se/fastqs/rep1/ENCFF744CHW.subsampled.400.fastq.gz" | ||
], | ||
"test_bowtie2.pe_bowtie2_idx_tar" : "atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar", | ||
"test_bowtie2.se_bowtie2_idx_tar" : "atac-seq-pipeline-test-data/genome_data/mm10_chr19_chrM/bowtie2_index/mm10_no_alt_analysis_set_ENCODE.chr19_chrM.fasta.tar", | ||
"test_bowtie2.pe_bowtie2_idx_tar" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/bowtie2_index/GRCh38_no_alt_analysis_set_GCA_000001405.15.chr19_chrM.fasta.tar", | ||
"test_bowtie2.se_bowtie2_idx_tar" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/mm10_chr19_chrM/bowtie2_index/mm10_no_alt_analysis_set_ENCODE.chr19_chrM.fasta.tar", | ||
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"test_bowtie2.se_chrsz" : "atac-seq-pipeline-test-data/genome_data/mm10_chr19_chrM/mm10_chr19_chrM.chrom.sizes", | ||
"test_bowtie2.pe_chrsz" : "atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes", | ||
"test_bowtie2.se_chrsz" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/mm10_chr19_chrM/mm10_chr19_chrM.chrom.sizes", | ||
"test_bowtie2.pe_chrsz" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/genome_data/hg38_chr19_chrM/hg38_chr19_chrM.chrom.sizes", | ||
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"test_bowtie2.ref_pe_flagstat" : "atac-seq-pipeline-test-data/ref_output/test_bowtie2/pe/multimapping/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.samstats.qc", | ||
"test_bowtie2.ref_pe_flagstat_no_multimapping" : "atac-seq-pipeline-test-data/ref_output/test_bowtie2/pe/no_multimapping/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.samstats.qc", | ||
"test_bowtie2.ref_se_flagstat" : "atac-seq-pipeline-test-data/ref_output/test_bowtie2/se/multimapping/merge_fastqs_R1_ENCFF439VSY.subsampled.400.trim.merged.samstats.qc", | ||
"test_bowtie2.ref_se_flagstat_no_multimapping" : "atac-seq-pipeline-test-data/ref_output/test_bowtie2/se/no_multimapping/merge_fastqs_R1_ENCFF439VSY.subsampled.400.trim.merged.samstats.qc", | ||
"test_bowtie2.ref_pe_flagstat" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bowtie2/pe/multimapping/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.samstats.qc", | ||
"test_bowtie2.ref_pe_flagstat_no_multimapping" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bowtie2/pe/no_multimapping/merge_fastqs_R1_ENCFF341MYG.subsampled.400.trim.merged.samstats.qc", | ||
"test_bowtie2.ref_se_flagstat" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bowtie2/se/multimapping/merge_fastqs_R1_ENCFF439VSY.subsampled.400.trim.merged.samstats.qc", | ||
"test_bowtie2.ref_se_flagstat_no_multimapping" : "gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/atac-seq-pipeline-test-data/ref_output/test_bowtie2/se/no_multimapping/merge_fastqs_R1_ENCFF439VSY.subsampled.400.trim.merged.samstats.qc", | ||
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"test_bowtie2.multimapping" : 4 | ||
} |
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