From 384e4ef6203b04481d8641ed406dd0776d6bd473 Mon Sep 17 00:00:00 2001 From: Dominik <dominik.brilhaus@hhu.de> Date: Fri, 24 Mar 2023 12:40:49 +0100 Subject: [PATCH] docker-free kallisto quant --- runs/kallisto_quant/run.cwl | 77 +++++++++++++--------- runs/kallisto_quant/run.yml | 3 + workflows/kallisto_quant/kallisto_quant.sh | 18 +---- workflows/kallisto_quant/workflow.cwl | 53 --------------- workflows/kallisto_sleuth/workflow.cwl | 33 ---------- 5 files changed, 50 insertions(+), 134 deletions(-) delete mode 100644 workflows/kallisto_quant/workflow.cwl delete mode 100644 workflows/kallisto_sleuth/workflow.cwl diff --git a/runs/kallisto_quant/run.cwl b/runs/kallisto_quant/run.cwl index af2bc99..980dc14 100644 --- a/runs/kallisto_quant/run.cwl +++ b/runs/kallisto_quant/run.cwl @@ -1,36 +1,49 @@ #!/usr/bin/env cwl-runner + cwlVersion: v1.2 -class: Workflow +class: CommandLineTool + inputs: - out_folder: - type: string - in_kallisto_index: - type: File - in_fastq_dir: - type: Directory - kallisto_bootstrap: - type: int - kallisto_threads: - type: int - kallisto_fragmentLength: - type: int - kallisto_stdDev: - type: int +- id: sh_script + type: File + inputBinding: + position: 0 +- id: out_folder + type: string + inputBinding: + position: 1 +- id: in_kallisto_index + type: File + inputBinding: + position: 2 +- id: in_fastq_dir + type: Directory + inputBinding: + position: 3 +- id: kallisto_bootstrap + type: int + inputBinding: + position: 4 +- id: kallisto_threads + type: int + inputBinding: + position: 5 +- id: kallisto_fragmentLength + type: int + inputBinding: + position: 6 +- id: kallisto_stdDev + type: int + inputBinding: + position: 7 + outputs: - out_dir: - type: - type: array - items: Directory - outputSource: kallisto_quant/outdir -steps: - kallisto_quant: - run: ../../workflows/kallisto_quant/workflow.cwl - in: - out_folder: out_folder - in_kallisto_index: in_kallisto_index - in_fastq_dir: in_fastq_dir - kallisto_bootstrap: kallisto_bootstrap - kallisto_threads: kallisto_threads - kallisto_fragmentLength: kallisto_fragmentLength - kallisto_stdDev: kallisto_stdDev - out: [outdir] +- id: outdir + type: + type: array + items: Directory + outputBinding: + glob: $(runtime.outdir)/$(inputs.out_folder) + +baseCommand: +- bash diff --git a/runs/kallisto_quant/run.yml b/runs/kallisto_quant/run.yml index e5c7505..09afef4 100644 --- a/runs/kallisto_quant/run.yml +++ b/runs/kallisto_quant/run.yml @@ -1,4 +1,7 @@ cores: 4 +sh_script: + class: File + path: ../../workflows/kallisto_quant/kallisto_quant.sh out_folder: ./kallisto_results in_kallisto_index: class: File diff --git a/workflows/kallisto_quant/kallisto_quant.sh b/workflows/kallisto_quant/kallisto_quant.sh index 124698c..63d0cb1 100644 --- a/workflows/kallisto_quant/kallisto_quant.sh +++ b/workflows/kallisto_quant/kallisto_quant.sh @@ -3,19 +3,6 @@ ### Map RNASeq reads via kallisto ### Note, this is written for single-end mode only -################################################ -#### CWL-independent tests -################################################ - -# arc_root=/Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq -# out_folder=runs/kallisto_quant/kallisto_results_v48_anaconda -# in_kallisto_index=runs/kallisto_index/kallisto_index -# in_fastq_folder=assays/Talinum_RNASeq_minimal/dataset -# kallisto_bootstrap=100 -# kallisto_threads=4 -# kallisto_fragmentLength=200 -# kallisto_stdDev=20 - ################################################ #### Read arguments from CLI ################################################ @@ -45,9 +32,8 @@ fastq_files=$(ls "${in_fastq_folder}"/*fastq*) ################################################ for j in $fastq_files; do - - # cut away path. retain only first six chars of file name - sampleName=$(echo $j | sed -e 's|.*/||' | sed -e 's|.fastq.*||') + + sampleName=$(basename $j) echo $sampleName diff --git a/workflows/kallisto_quant/workflow.cwl b/workflows/kallisto_quant/workflow.cwl deleted file mode 100644 index 1041d73..0000000 --- a/workflows/kallisto_quant/workflow.cwl +++ /dev/null @@ -1,53 +0,0 @@ -#!/usr/bin/env cwl-runner -cwlVersion: v1.2 -class: CommandLineTool -hints: - DockerRequirement: - dockerPull: zlskidmore/kallisto:0.48.0 -requirements: -- class: InitialWorkDirRequirement - listing: - - class: File - location: kallisto_quant.sh -baseCommand: -- bash -arguments: -- position: 0 - valueFrom: ./kallisto_quant.sh -inputs: -- id: out_folder - type: string - inputBinding: - position: 1 -- id: in_kallisto_index - type: File - inputBinding: - position: 2 -- id: in_fastq_dir - type: Directory - inputBinding: - position: 3 -- id: kallisto_bootstrap - type: int - inputBinding: - position: 4 -- id: kallisto_threads - type: int - inputBinding: - position: 5 -- id: kallisto_fragmentLength - type: int - inputBinding: - position: 6 -- id: kallisto_stdDev - type: int - inputBinding: - position: 7 - -outputs: -- id: outdir - type: - type: array - items: Directory - outputBinding: - glob: $(runtime.outdir)/$(inputs.out_folder) diff --git a/workflows/kallisto_sleuth/workflow.cwl b/workflows/kallisto_sleuth/workflow.cwl deleted file mode 100644 index 48ac0b1..0000000 --- a/workflows/kallisto_sleuth/workflow.cwl +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env cwl-runner - -cwlVersion: v1.2 -class: CommandLineTool -hints: - DockerRequirement: - dockerPull: zimmera95/rnaseq:latest -requirements: - - class: InitialWorkDirRequirement - listing: - - class: File - location: kallisto_sleuth.R -baseCommand: -- Rscript -arguments: - - position: 0 - valueFrom: kallisto_sleuth.R -inputs: - - id: in_sleuth - type: File - inputBinding: - position: 1 - - id: out_folder - type: string - inputBinding: - position: 2 -outputs: -- id: outdir - type: - type: array - items: Directory - outputBinding: - glob: $(runtime.outdir)/$(inputs.out_folder) -- GitLab