diff --git a/workflows/kallisto/README.md b/workflows/kallisto/README.md deleted file mode 100644 index 244a3c13bfec41dce6d7e5e892b1b5e37fe55d2f..0000000000000000000000000000000000000000 --- a/workflows/kallisto/README.md +++ /dev/null @@ -1,12 +0,0 @@ - -# Kallisto - -CWL adapted from: https://github.com/common-workflow-library/bio-cwl-tools/commit/91c42fb809ce18eafe16155cca0abf362270c0fe - -## Workflow graph - -```bash -cwltool --print-dot kallisto-workflow.cwl | dot -Tsvg > kallisto_workflow_graph.svg -``` - - \ No newline at end of file diff --git a/workflows/kallisto/kallisto-help.cwl b/workflows/kallisto/kallisto-test.cwl similarity index 100% rename from workflows/kallisto/kallisto-help.cwl rename to workflows/kallisto/kallisto-test.cwl diff --git a/workflows/kallisto/kallisto_workflow_graph.svg b/workflows/kallisto/kallisto_workflow_graph.svg deleted file mode 100644 index a9083cee1ed9f5c8f89da0ff9cfcd795b28818aa..0000000000000000000000000000000000000000 --- 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class="cluster"> -<title>cluster_outputs</title> -<polygon fill="#eeeeee" stroke="black" stroke-dasharray="5,2" points="310,-8 310,-84 456,-84 456,-8 310,-8"/> -<text text-anchor="middle" x="383" y="-15.8" font-family="Times,serif" font-size="14.00">Workflow Outputs</text> -</g> -<!-- quant --> -<g id="node1" class="node"> -<title>quant</title> -<polygon fill="lightgoldenrodyellow" stroke="black" points="647,-185.5 647,-221.5 705,-221.5 705,-185.5 647,-185.5"/> -<text text-anchor="middle" x="676" y="-199.8" font-family="Times,serif" font-size="14.00">quant</text> -</g> -<!-- collectResults --> -<g id="node2" class="node"> -<title>collectResults</title> -<polygon fill="lightgoldenrodyellow" stroke="black" points="325,-112.5 325,-148.5 441,-148.5 441,-112.5 325,-112.5"/> -<text text-anchor="middle" x="383" y="-126.8" font-family="Times,serif" font-size="14.00">collectResults</text> -</g> -<!-- quant->collectResults --> -<g id="edge1" class="edge"> -<title>quant->collectResults</title> 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text-anchor="middle" x="194" y="-272.8" font-family="Times,serif" font-size="14.00">index</text> -</g> -<!-- index->quant --> -<g id="edge2" class="edge"> -<title>index->quant</title> -<path fill="none" stroke="black" d="M222.35,-271.32C304.43,-259.23 542.41,-224.18 636.78,-210.28"/> -<polygon fill="black" stroke="black" points="637.39,-213.73 646.77,-208.81 636.37,-206.8 637.39,-213.73"/> -</g> -<!-- resultsFolder --> -<g id="node4" class="node"> -<title>resultsFolder</title> -<polygon fill="#94ddf4" stroke="black" points="16,-334.5 16,-370.5 128,-370.5 128,-334.5 16,-334.5"/> -<text text-anchor="middle" x="72" y="-348.8" font-family="Times,serif" font-size="14.00">resultsFolder</text> -</g> -<!-- resultsFolder->collectResults --> -<g id="edge3" class="edge"> -<title>resultsFolder->collectResults</title> -<path fill="none" stroke="black" d="M84.72,-334.44C100.23,-314.43 127.98,-281.07 157,-258 213.1,-213.41 286.94,-175.31 334.69,-152.9"/> -<polygon fill="black" stroke="black" points="336.29,-156.02 343.88,-148.63 333.34,-149.67 336.29,-156.02"/> -</g> -<!-- IndexInput --> -<g id="node5" class="node"> -<title>IndexInput</title> -<polygon fill="#94ddf4" stroke="black" points="146.5,-334.5 146.5,-370.5 241.5,-370.5 241.5,-334.5 146.5,-334.5"/> -<text text-anchor="middle" x="194" y="-348.8" font-family="Times,serif" font-size="14.00">IndexInput</text> -</g> -<!-- IndexInput->index --> -<g id="edge4" class="edge"> -<title>IndexInput->index</title> -<path fill="none" stroke="black" d="M188.2,-334.34C187.27,-325.56 187.02,-314.66 187.46,-304.77"/> -<polygon fill="black" stroke="black" points="190.97,-304.8 188.21,-294.57 183.99,-304.29 190.97,-304.8"/> -</g> -<!-- IndexInput->index --> -<g id="edge5" class="edge"> -<title>IndexInput->index</title> -<path fill="none" stroke="black" d="M199.8,-334.34C200.73,-325.56 200.98,-314.66 200.54,-304.77"/> -<polygon fill="black" stroke="black" points="204.01,-304.29 199.79,-294.57 197.03,-304.8 204.01,-304.29"/> -</g> -<!-- BootstrapSamples --> -<g id="node6" class="node"> -<title>BootstrapSamples</title> -<polygon fill="#94ddf4" stroke="black" points="260,-334.5 260,-370.5 408,-370.5 408,-334.5 260,-334.5"/> -<text text-anchor="middle" x="334" y="-348.8" font-family="Times,serif" font-size="14.00">BootstrapSamples</text> -</g> -<!-- BootstrapSamples->quant --> -<g id="edge6" class="edge"> -<title>BootstrapSamples->quant</title> -<path fill="none" stroke="black" d="M361.03,-334.43C377.21,-324.58 398.38,-312.33 418,-303 493.49,-267.08 585.84,-234.39 637.06,-217.2"/> -<polygon fill="black" stroke="black" points="638.36,-220.46 646.74,-213.97 636.15,-213.81 638.36,-220.46"/> -</g> -<!-- FragmentLength --> -<g id="node7" class="node"> -<title>FragmentLength</title> -<polygon fill="#94ddf4" stroke="black" points="426.5,-334.5 426.5,-370.5 563.5,-370.5 563.5,-334.5 426.5,-334.5"/> -<text text-anchor="middle" x="495" y="-348.8" font-family="Times,serif" font-size="14.00">FragmentLength</text> -</g> -<!-- 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class="node"> -<title>isSingle</title> -<polygon fill="#94ddf4" stroke="black" points="751,-334.5 751,-370.5 825,-370.5 825,-334.5 751,-334.5"/> -<text text-anchor="middle" x="788" y="-348.8" font-family="Times,serif" font-size="14.00">isSingle</text> -</g> -<!-- isSingle->quant --> -<g id="edge9" class="edge"> -<title>isSingle->quant</title> -<path fill="none" stroke="black" d="M775.14,-334.23C766.7,-323.94 754.87,-311.31 742,-303 732.91,-297.13 727.06,-302.23 719,-295 700.25,-278.19 688.96,-251.45 682.68,-231.39"/> -<polygon fill="black" stroke="black" points="685.99,-230.23 679.84,-221.59 679.26,-232.17 685.99,-230.23"/> -</g> -<!-- numUnderscoresFileName --> -<g id="node10" class="node"> -<title>numUnderscoresFileName</title> -<polygon fill="#94ddf4" stroke="black" points="843,-334.5 843,-370.5 1051,-370.5 1051,-334.5 843,-334.5"/> -<text text-anchor="middle" x="947" y="-348.8" font-family="Times,serif" font-size="14.00">numUnderscoresFileName</text> -</g> -<!-- numUnderscoresFileName->quant --> -<g id="edge10" class="edge"> -<title>numUnderscoresFileName->quant</title> -<path fill="none" stroke="black" d="M914.31,-334.34C892.23,-323.54 862.1,-310.31 834,-303 800.7,-294.34 787.64,-310.65 757,-295 749.29,-291.06 718.14,-254.93 696.79,-229.53"/> -<polygon fill="black" stroke="black" points="699.35,-227.14 690.25,-221.72 693.99,-231.63 699.35,-227.14"/> -</g> -<!-- InputReadsMultipleSamples --> -<g id="node11" class="node"> -<title>InputReadsMultipleSamples</title> -<polygon fill="#94ddf4" stroke="black" points="1069.5,-334.5 1069.5,-370.5 1288.5,-370.5 1288.5,-334.5 1069.5,-334.5"/> -<text text-anchor="middle" x="1179" y="-348.8" font-family="Times,serif" font-size="14.00">InputReadsMultipleSamples</text> -</g> -<!-- InputReadsMultipleSamples->quant --> -<g id="edge11" class="edge"> -<title>InputReadsMultipleSamples->quant</title> -<path fill="none" stroke="black" d="M1133.09,-334.43C1108.8,-324.46 1078.54,-312.1 1051,-303 930.41,-263.16 784.15,-229.58 715.25,-213.93"/> -<polygon fill="black" stroke="black" points="715.79,-210.46 705.27,-211.66 714.25,-217.29 715.79,-210.46"/> -</g> -<!-- InputReadsMultipleSamples->quant --> -<g id="edge12" class="edge"> -<title>InputReadsMultipleSamples->quant</title> -<path fill="none" stroke="black" d="M1148.73,-334.43C1126.8,-324.46 1096.54,-312.1 1069,-303 941.93,-261.02 786.37,-225.99 714.95,-211.57"/> -<polygon fill="black" stroke="black" points="715.53,-208.11 705.04,-209.59 714.16,-214.98 715.53,-208.11"/> -</g> -</g> -</svg> diff --git a/workflows/kallisto/yield-dirInDestination.cwl b/workflows/kallisto/yield-dirInDestination.cwl index c2a20eabcd7bfc412238d74a99aedb6eac468008..bc90cb81f1a907735bd433d6117c55872c213f92 100644 --- a/workflows/kallisto/yield-dirInDestination.cwl +++ b/workflows/kallisto/yield-dirInDestination.cwl @@ -1,7 +1,7 @@ cwlVersion: v1.2 class: ExpressionTool doc: | - Takes a directory (e.g. from a workflow step) and yield it in a desired directory. + Takes a directory (e.g. from a workflow step) and yields it in a desired directory. requirements: - class: InlineJavascriptRequirement inputs: