Dsl2 refactor #338
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -70,10 +70,6 @@ process { | |
| memory = {params.max_memory} | ||
| } | ||
|
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||
| withName:CONCAT_VCF { | ||
| // For unknown reasons, CONCAT_VCF sometimes fails with SIGPIPE | ||
| // (exit code 141). Rerunning the process will usually work. | ||
|
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@@ -89,12 +85,4 @@ process { | |
| withName:MULTIQC { | ||
| errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -9,63 +9,76 @@ params { | |
| // BUILD_INDICES | ||
| 'build_intervals' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'bwa_index' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'bwamem2_index' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'create_intervals_bed' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'dict' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'index_target_bed' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'msisensor_scan' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'samtools_faidx' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'tabix_dbsnp' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'tabix_germline_resource' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'tabix_known_indels' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| 'tabix_pon' { | ||
| publish_dir = "reference" | ||
| publish_files = false | ||
| } | ||
| // MAPPING | ||
| 'bwa_mem1_mem' { | ||
| args = "-K 100000000 -M" | ||
| args2 = "sort" | ||
| publish_files = false | ||
| } | ||
| 'bwa_mem1_mem_tumor' { | ||
| args = "-K 100000000 -M -B 3" | ||
| args2 = "sort" | ||
| publish_files = false | ||
| } | ||
| 'bwa_mem2_mem' { | ||
| args = "-K 100000000 -M" | ||
| args2 = "sort" | ||
| publish_files = false | ||
| } | ||
| 'bwa_mem2_mem_tumor' { | ||
| args = "-K 100000000 -M -B 3" | ||
| args2 = "sort" | ||
| publish_files = false | ||
| } | ||
| 'merge_bam_mapping' { | ||
| publish_by_id = "true" | ||
| publish_files = ['bam':'mapped'] | ||
| publish_dir = "preprocessing" | ||
| } | ||
| 'qualimap_bamqc_mapping' { | ||
|
|
@@ -74,6 +87,7 @@ params { | |
| } | ||
| 'samtools_index_mapping' { | ||
| publish_by_id = "true" | ||
| publish_files = ['bai':'mapped'] | ||
| publish_dir = "preprocessing" | ||
| } | ||
| 'samtools_stats_mapping' { | ||
|
|
@@ -108,6 +122,7 @@ params { | |
| 'merge_bam_recalibrate' { | ||
| suffix = "recal" | ||
| publish_by_id = "true" | ||
| publish_files = ['bam':'recalibrated'] | ||
| publish_dir = "preprocessing" | ||
| } | ||
| 'qualimap_bamqc_recalibrate' { | ||
|
|
@@ -128,12 +143,12 @@ params { | |
| 'haplotypecaller' { | ||
| publish_by_id = "true" | ||
| publish_dir = "variant_calling" | ||
| publish_files = false | ||
| } | ||
| 'genotypegvcf' { | ||
| publish_by_id = "true" | ||
| publish_dir = "variant_calling" | ||
| publish_files = false | ||
| } | ||
| 'concat_haplotypecaller' { | ||
| suffix = "haplotypecaller" | ||
|
|
||
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is this now running on all branches? or none?