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Fix output collector #8

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Merged
rhshah merged 1 commit into from
May 4, 2017
Merged

Fix output collector #8

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6 changes: 3 additions & 3 deletions mutect/outputs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ outputs:
outputBinding:
glob: |
${
if (inputs.inputVcf )
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.vcf';
if (inputs.inputVcf)
return inputs.inputVcf.basename.replace(".vcf","_STDfilter.vcf");
return null;
}
txt:
Expand All @@ -14,6 +14,6 @@ outputs:
glob: |
${
if (inputs.inputTxt)
return inputs.inputTxt.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
return inputs.inputTxt.basename.replace(".txt","_STDfilter.txt");
return null;
}
6 changes: 3 additions & 3 deletions pindel/outputs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ outputs:
outputBinding:
glob: |
${
if (inputs.inputVcf )
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.vcf';
if (inputs.inputVcf)
return inputs.inputVcf.basename.replace(".vcf","_STDfilter.vcf");
return null;
}
txt:
Expand All @@ -14,6 +14,6 @@ outputs:
glob: |
${
if (inputs.inputVcf)
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
return inputs.inputVcf.basename.replace(".vcf","_STDfilter.txt");
return null;
}
8 changes: 4 additions & 4 deletions somaticindeldetector/outputs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,16 @@ outputs:
outputBinding:
glob: |
${
if (inputs.inputVcf )
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.vcf';
if (inputs.inputVcf)
return inputs.inputVcf.basename.replace(".vcf","_STDfilter.vcf");
return null;
}
txt:
type: File
outputBinding:
glob: |
${
if (inputs.inputVcf)
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
if (inputs.inputTxt)
return inputs.inputTxt.basename.replace(".txt","_STDfilter.txt");
return null;
}
6 changes: 3 additions & 3 deletions vardict/outputs.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@ outputs:
outputBinding:
glob: |
${
if (inputs.inputVcf )
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.vcf';
if (inputs.inputVcf)
return inputs.inputVcf.basename.replace(".vcf","_STDfilter.vcf");
return null;
}
txt:
Expand All @@ -14,6 +14,6 @@ outputs:
glob: |
${
if (inputs.inputVcf)
return inputs.inputVcf.replace(/^.*[\\\/]/, '').replace(/\.[^/.]+$/, '').replace(/\.vcf/,'') + '_STDfilter.txt';
return inputs.inputVcf.basename.replace(".vcf","_STDfilter.txt");
return null;
}