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Merge pull request #14 from 4dn-dcic/dev
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,98 @@ | ||
| { | ||
| "hints": [ | ||
| { | ||
| "dockerPull": "duplexa/4dn-repliseq:v9", | ||
| "class": "DockerRequirement" | ||
| } | ||
| ], | ||
| "arguments": [], | ||
| "class": "CommandLineTool", | ||
| "inputs": [ | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#fastq1", | ||
| "inputBinding": { | ||
| "position": 1, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#fastq2", | ||
| "inputBinding": { | ||
| "position": 2, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#bwa_index", | ||
| "inputBinding": { | ||
| "position": 3, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "int" | ||
| ], | ||
| "id": "#nThreads", | ||
| "inputBinding": { | ||
| "position": 6, | ||
| "separate": true | ||
| }, | ||
| "default": 4 | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#prefix", | ||
| "inputBinding": { | ||
| "position": 5, | ||
| "separate": true | ||
| }, | ||
| "default": "out" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#outdir", | ||
| "inputBinding": { | ||
| "position": 4, | ||
| "separate": true | ||
| }, | ||
| "default": "." | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#out_bam", | ||
| "outputBinding": { | ||
| "glob": "*.bam" | ||
| } | ||
| } | ||
| ], | ||
| "baseCommand": [ | ||
| "run-align-pe.sh" | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "cwlVersion": "draft-3" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| { | ||
| "hints": [ | ||
| { | ||
| "dockerPull": "duplexa/4dn-repliseq:v9", | ||
| "class": "DockerRequirement" | ||
| } | ||
| ], | ||
| "arguments": [], | ||
| "class": "CommandLineTool", | ||
| "inputs": [ | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#fastq1", | ||
| "inputBinding": { | ||
| "position": 1, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#bwa_index", | ||
| "inputBinding": { | ||
| "position": 2, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "int" | ||
| ], | ||
| "id": "#nThreads", | ||
| "inputBinding": { | ||
| "position": 5, | ||
| "separate": true | ||
| }, | ||
| "default": 4 | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#prefix", | ||
| "inputBinding": { | ||
| "position": 4, | ||
| "separate": true | ||
| }, | ||
| "default": "out" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#outdir", | ||
| "inputBinding": { | ||
| "position": 3, | ||
| "separate": true | ||
| }, | ||
| "default": "." | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#out_bam", | ||
| "outputBinding": { | ||
| "glob": "*.bam" | ||
| } | ||
| } | ||
| ], | ||
| "baseCommand": [ | ||
| "run-align-se.sh" | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "cwlVersion": "draft-3" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| { | ||
| "hints": [ | ||
| { | ||
| "dockerPull": "duplexa/4dn-repliseq:v9", | ||
| "class": "DockerRequirement" | ||
| } | ||
| ], | ||
| "arguments": [], | ||
| "class": "CommandLineTool", | ||
| "inputs": [ | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#input_fastq", | ||
| "inputBinding": { | ||
| "position": 1, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#outprefix", | ||
| "inputBinding": { | ||
| "position": 2, | ||
| "separate": true | ||
| }, | ||
| "default": "out" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#outdir", | ||
| "inputBinding": { | ||
| "position": 1, | ||
| "separate": true | ||
| }, | ||
| "default": "." | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#out_clipped_fastq", | ||
| "outputBinding": { | ||
| "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.clip.fastq')" | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#out_log", | ||
| "outputBinding": { | ||
| "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.clip.fastq.log')" | ||
| } | ||
| } | ||
| ], | ||
| "baseCommand": [ | ||
| "clip" | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "cwlVersion": "draft-3" | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,100 @@ | ||
| { | ||
| "hints": [ | ||
| { | ||
| "dockerPull": "duplexa/4dn-repliseq:v9", | ||
| "class": "DockerRequirement" | ||
| } | ||
| ], | ||
| "arguments": [], | ||
| "class": "CommandLineTool", | ||
| "inputs": [ | ||
| { | ||
| "type": [ | ||
| "File" | ||
| ], | ||
| "id": "#input_bam", | ||
| "inputBinding": { | ||
| "position": 1, | ||
| "separate": true | ||
| } | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 2 | ||
| }, | ||
| "id": "#chrsizes" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "int" | ||
| ], | ||
| "id": "#winsize", | ||
| "inputBinding": { | ||
| "position": 5, | ||
| "separate": true | ||
| }, | ||
| "default": 5000 | ||
| }, | ||
| { | ||
| "type": [ | ||
| "int" | ||
| ], | ||
| "id": "#minsize", | ||
| "inputBinding": { | ||
| "position": 6, | ||
| "separate": true | ||
| }, | ||
| "default": 10000000 | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#outprefix", | ||
| "inputBinding": { | ||
| "position": 4, | ||
| "separate": true | ||
| }, | ||
| "default": "out" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "id": "#outdir", | ||
| "inputBinding": { | ||
| "position": 3, | ||
| "separate": true | ||
| }, | ||
| "default": "." | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#out_count_bg", | ||
| "outputBinding": { | ||
| "glob": "$(inputs.outdir + '/' + inputs.outprefix + '.w' + inputs.winsize + '.bg')" | ||
| } | ||
| } | ||
| ], | ||
| "baseCommand": [ | ||
| "count" | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "cwlVersion": "draft-3" | ||
| } |
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