diff --git a/runs/kallisto_index/run.cwl b/runs/kallisto_index/run.cwl index a115ab7926f4c454ce8b95bc642571030b957066..a8665ac38a52da961f0dc10751bedaef0451c8bd 100644 --- a/runs/kallisto_index/run.cwl +++ b/runs/kallisto_index/run.cwl @@ -1,21 +1,29 @@ #!/usr/bin/env cwl-runner + cwlVersion: v1.2 -class: Workflow +class: CommandLineTool + inputs: - in_genome_ref: - type: File - out_folder: - type: string +- id: sh_script + type: File + inputBinding: + position: 0 +- id: in_genome_ref + type: File + inputBinding: + position: 2 +- id: out_folder + type: string + inputBinding: + position: 3 + outputs: - out_dir: - type: - type: array - items: Directory - outputSource: kallisto_index/outdir -steps: - kallisto_index: - run: ../../workflows/kallisto_index/workflow.cwl - in: - in_genome_ref: in_genome_ref - out_folder: out_folder - out: [outdir] +- id: outdir + type: + type: array + items: Directory + outputBinding: + glob: $(runtime.outdir)/$(inputs.out_folder) + +baseCommand: +- bash diff --git a/runs/kallisto_index/run.yml b/runs/kallisto_index/run.yml index 37c668126ba083e52faee307fecd8ce59af2c0ba..df0c0706df4bcbda3746868761ef252449eb736c 100644 --- a/runs/kallisto_index/run.yml +++ b/runs/kallisto_index/run.yml @@ -1,4 +1,7 @@ cores: 1 +sh_script: + class: File + path: ../../workflows/kallisto_index/kallisto_index.sh in_genome_ref: class: File path: ../../studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa diff --git a/workflows/kallisto_collect/workflow.cwl b/workflows/kallisto_collect/workflow.cwl deleted file mode 100644 index b5ed0f7fe34a6a740b6986efc079473186ad0c11..0000000000000000000000000000000000000000 --- a/workflows/kallisto_collect/workflow.cwl +++ /dev/null @@ -1,44 +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_collect.R -baseCommand: -- Rscript -arguments: - - position: 0 - valueFrom: kallisto_collect.R -inputs: -- id: in_kallisto_results - type: Directory - inputBinding: - position: 1 -- id: in_metadata_file - type: File - inputBinding: - position: 2 -- id: in_metadata_sample - type: string - inputBinding: - position: 3 -- id: in_metadata_factor - type: string - inputBinding: - position: 4 -- id: out_folder - type: string - inputBinding: - position: 5 -outputs: -- id: outdir - type: - type: array - items: Directory - outputBinding: - glob: $(runtime.outdir)/$(inputs.out_folder) diff --git a/workflows/kallisto_index/kallisto_index.sh b/workflows/kallisto_index/kallisto_index.sh index c7cb12d292e64b8334a4cb1a80a833023c226dc6..c346206eca3c0d7ec2294deb2387573e8d7926f8 100644 --- a/workflows/kallisto_index/kallisto_index.sh +++ b/workflows/kallisto_index/kallisto_index.sh @@ -2,16 +2,6 @@ ### Build kallisto index - -################################################ -#### CWL-independent tests -################################################ - -# in_genome_ref=studies/TalinumGenomeDraft/resources/Talinum.gm.CDS.nt.fa -# out_folder=runs/kallisto_index -# arc_root=/Users/dominikbrilhaus/gitlab_dataplant/samplearc_rnaseq - - ################################################ #### Read arguments from CLI ################################################ diff --git a/workflows/kallisto_index/workflow.cwl b/workflows/kallisto_index/workflow.cwl deleted file mode 100644 index 32635f746d02b1061a0fe8d020045d2afe93b399..0000000000000000000000000000000000000000 --- a/workflows/kallisto_index/workflow.cwl +++ /dev/null @@ -1,32 +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_index.sh -baseCommand: -- bash -arguments: - - position: 0 - valueFrom: ./kallisto_index.sh -inputs: -- id: in_genome_ref - 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)