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Merge pull request #9 from 4dn-dcic/dev
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,80 @@ | ||
| { | ||
| "baseCommand": [ | ||
| "pipeline_Sorted2noDups.sh" | ||
| ], | ||
| "inputs": [ | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 1 | ||
| }, | ||
| "id": "#pairsam" | ||
| }, | ||
| { | ||
| "default": "out", | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 2 | ||
| }, | ||
| "id": "#outprefix" | ||
| }, | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "outputBinding": { | ||
| "glob": "$(outprefix + '.lossless.bam')" | ||
| }, | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#lossless_bamfile" | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "outputBinding": { | ||
| "glob": "$(outprefix + '.dedup.pairs.gz')" | ||
| }, | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#dedup_pairs" | ||
| } | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "outputBinding": { | ||
| "glob": "$(outprefix + '.unmapped.sam.pairs.gz')" | ||
| }, | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#unmapped_pairsam" | ||
| } | ||
| ], | ||
| "cwlVersion": "draft-3", | ||
| "hints": [ | ||
| { | ||
| "dockerPull": "duplexa/4dn-hic:v35", | ||
| "class": "DockerRequirement" | ||
| } | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "arguments": [], | ||
| "class": "CommandLineTool" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| { | ||
| "baseCommand": [ | ||
| "pairsam-markasdup.sh" | ||
| ], | ||
| "inputs": [ | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 1 | ||
| }, | ||
| "id": "#pairsam" | ||
| }, | ||
| { | ||
| "default": "out", | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 2 | ||
| }, | ||
| "id": "#outprefix" | ||
| }, | ||
| ], | ||
| "outputs": [ | ||
| { | ||
| "outputBinding": { | ||
| "glob": "$(inputs.outprefix + '.marked.sam.pairs.gz')" | ||
| }, | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#out_markedpairs" | ||
| } | ||
| ], | ||
| "cwlVersion": "draft-3", | ||
| "hints": [ | ||
| { | ||
| "dockerPull": "duplexa/4dn-hic:v40", | ||
| "class": "DockerRequirement" | ||
| } | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "arguments": [], | ||
| "class": "CommandLineTool" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| { | ||
| "baseCommand": [ | ||
| "pairsam-merge.sh" | ||
| ], | ||
| "inputs": [ | ||
| { | ||
| "default": "out", | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 1 | ||
| }, | ||
| "id": "#outprefix" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "int" | ||
| ], | ||
| "id": "#nThreads", | ||
| "inputBinding": { | ||
| "position": 2, | ||
| "separate": true | ||
| }, | ||
| "default": 8 | ||
| }, | ||
| { | ||
| "id": "#input_pairs", | ||
| "inputBinding": { | ||
| "itemSeparator": " ", | ||
| "position": 3, | ||
| "separate": true | ||
| }, | ||
| "type": [ | ||
| "null", | ||
| { | ||
| "items": "File", | ||
| "type": "array" | ||
| } | ||
| ] | ||
| } | ||
|
|
||
| ], | ||
| "outputs": [ | ||
| { | ||
| "outputBinding": { | ||
| "glob": "$(inputs.outprefix + '.merged.sam.pairs.gz')" | ||
| }, | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#merged_pairs" | ||
| } | ||
| ], | ||
| "cwlVersion": "draft-3", | ||
| "hints": [ | ||
| { | ||
| "dockerPull": "duplexa/4dn-hic:v40", | ||
| "class": "DockerRequirement" | ||
| } | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "arguments": [], | ||
| "class": "CommandLineTool" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,90 @@ | ||
| { | ||
| "baseCommand": [ | ||
| "pairsam-parse-sort.sh" | ||
| ], | ||
| "inputs": [ | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 1 | ||
| }, | ||
| "id": "#bam" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 3 | ||
| }, | ||
| "id": "#chromsize" | ||
| }, | ||
| { | ||
| "default": "out", | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 2 | ||
| }, | ||
| "id": "#outprefix" | ||
| }, | ||
| { | ||
| "type": [ | ||
| "int" | ||
| ], | ||
| "id": "#Threads", | ||
| "inputBinding": { | ||
| "position": 4, | ||
| "separate": true | ||
| }, | ||
| "default": 8 | ||
| }, | ||
| { "default": "lz4c", | ||
| "type": [ | ||
| "null", | ||
| "string" | ||
| ], | ||
| "inputBinding": { | ||
| "separate": true, | ||
| "position": 5 | ||
| }, | ||
| "id": "#compress_programm" | ||
| }, | ||
|
|
||
| ], | ||
| "outputs": [ | ||
| { | ||
| "outputBinding": { | ||
| "glob": "$(inputs.outprefix + '.sam.pairs.gz')" | ||
| }, | ||
| "type": [ | ||
| "null", | ||
| "File" | ||
| ], | ||
| "id": "#out_pairs" | ||
| } | ||
| ], | ||
| "cwlVersion": "draft-3", | ||
| "hints": [ | ||
| { | ||
| "dockerPull": "duplexa/4dn-hic:v40", | ||
| "class": "DockerRequirement" | ||
| } | ||
| ], | ||
| "requirements": [ | ||
| { | ||
| "class": "InlineJavascriptRequirement" | ||
| } | ||
| ], | ||
| "arguments": [], | ||
| "class": "CommandLineTool" | ||
| } |
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