From 267c5f24ec081a4a08e59607eda87264936bc160 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 12 Jan 2017 19:45:20 +0000 Subject: [PATCH 1/3] Added fix so that input json without a tar file works Added a fix so that input json without a tar file works --- docker/rnaseq-cgl-pipeline.cwl | 16 +++++----------- 1 file changed, 5 insertions(+), 11 deletions(-) diff --git a/docker/rnaseq-cgl-pipeline.cwl b/docker/rnaseq-cgl-pipeline.cwl index aca0107..426bacd 100644 --- a/docker/rnaseq-cgl-pipeline.cwl +++ b/docker/rnaseq-cgl-pipeline.cwl @@ -53,17 +53,11 @@ hints: description: "The process requires at least 16G of RAM and we recommend 500GB or storage." inputs: - #if no tar files are going to be input - #then use - # "sample-tar": [], - #in the parameterized JSON file sample-tar: - doc: "Absolute path(s) to sample tarballs" - type: - type: array - items: ["null", File] - inputBinding: - prefix: --sample-tar + doc: "Absolute path to sample tarball" + type: File[]? + inputBinding: + prefix: --sample-tar sample-single: doc: "Absolute path(s) to unpaired FASTQ files. FASTQ files are comma delimited. Ex: sample1,sample2,sample3,sample4" @@ -180,7 +174,7 @@ outputs: # items: ["null", File] items: File outputBinding: - glob: '*.bam' + glob: '*.sortedByCoord.md.bam' doc: "BAM result files RNA-seq CGL pipeline" baseCommand: ["--logDebug"] From 1839ee665e45d6027181a8567a1ddbb8ab606de4 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 12 Jan 2017 19:50:29 +0000 Subject: [PATCH 2/3] Fixed version of docker image to pull Fixed version of docker image to pull --- docker/rnaseq-cgl-pipeline.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/rnaseq-cgl-pipeline.cwl b/docker/rnaseq-cgl-pipeline.cwl index 426bacd..ecdc1a5 100644 --- a/docker/rnaseq-cgl-pipeline.cwl +++ b/docker/rnaseq-cgl-pipeline.cwl @@ -43,7 +43,7 @@ dct:creator: requirements: - class: DockerRequirement - dockerPull: "quay.io/ucsc_cgl/rnaseq-cgl-pipeline:3.0.2-1" + dockerPull: "quay.io/ucsc_cgl/rnaseq-cgl-pipeline:3.0.2-2" hints: - class: ResourceRequirement From 91a7f2275b9802eff799601affcf87764188c106 Mon Sep 17 00:00:00 2001 From: Walt Shands Date: Thu, 12 Jan 2017 20:13:45 +0000 Subject: [PATCH 3/3] Set output BAM glob to *.bam to capture both BAM names from pipeline Set output BAM glob to *.bam to capture both BAM names from pipeline --- docker/rnaseq-cgl-pipeline.cwl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docker/rnaseq-cgl-pipeline.cwl b/docker/rnaseq-cgl-pipeline.cwl index ecdc1a5..7605cec 100644 --- a/docker/rnaseq-cgl-pipeline.cwl +++ b/docker/rnaseq-cgl-pipeline.cwl @@ -174,7 +174,7 @@ outputs: # items: ["null", File] items: File outputBinding: - glob: '*.sortedByCoord.md.bam' + glob: '*.bam' doc: "BAM result files RNA-seq CGL pipeline" baseCommand: ["--logDebug"]