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Merge pull request #195 from wtsi-npg/devel
prep for release 0.19.0
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,130 @@ | ||
| { | ||
| "version":"1.0", | ||
| "description":"steps in the alignment pipeline perform a checksum-based comparison of input and output (bam) data. Final validation step in alignment pipeline", | ||
| "subgraph_io":{ | ||
| "ports":{ | ||
| "inputs":{ | ||
| "fastq1":"salmon:__FQ1_IN__", | ||
| "fastq2":"salmon:__FQ2_IN__" | ||
| } | ||
| } | ||
| }, | ||
| "subst_params":[ | ||
| { | ||
| "id":"salmon_dir", | ||
| "required":"no", | ||
| "default":"salmon_quant" | ||
| }, | ||
| { | ||
| "id":"salmon_out", | ||
| "required":"no", | ||
| "subst_constructor":{ | ||
| "vals":[ {"subst":"salmon_dir"}, "_", {"subst":"rpt"} ], | ||
| "postproc":{"op":"concat","pad":""} | ||
| } | ||
| }, | ||
| { | ||
| "id":"quant", | ||
| "required":"no", | ||
| "subst_constructor":{ | ||
| "vals":[ {"subst":"salmon_dir"}, "_", {"subst":"rpt"}, "/quant.sf" ], | ||
| "postproc":{"op":"concat","pad":""} | ||
| }, | ||
| "default":"salmon_quant/quant.sf" | ||
| }, | ||
| { | ||
| "id":"quant_genes", | ||
| "required":"no", | ||
| "subst_constructor":{ | ||
| "vals":[ {"subst":"salmon_dir"}, "_", {"subst":"rpt"}, "/quant.genes.sf" ], | ||
| "postproc":{"op":"concat","pad":""} | ||
| }, | ||
| "default":"salmon_quant/quant.genes.sf" | ||
| }, | ||
| { | ||
| "id":"lib_format_counts", | ||
| "required":"no", | ||
| "subst_constructor":{ | ||
| "vals":[ {"subst":"salmon_dir"}, "_", {"subst":"rpt"}, "/lib_format_counts.json" ], | ||
| "postproc":{"op":"concat","pad":""} | ||
| }, | ||
| "default":"salmon_quant/lib_format_counts.json" | ||
| }, | ||
| { | ||
| "id":"libparams", | ||
| "required":"no", | ||
| "subst_constructor":{ | ||
| "vals":[ {"subst":"salmon_dir"}, "_", {"subst":"rpt"}, "/libParams" ], | ||
| "postproc":{"op":"concat","pad":""} | ||
| }, | ||
| "default":"salmon_quant/libParams" | ||
| }, | ||
| { | ||
| "id":"cmd_info", | ||
| "required":"no", | ||
| "subst_constructor":{ | ||
| "vals":[ {"subst":"salmon_dir"}, "_", {"subst":"rpt"}, "/cmd_info.json" ], | ||
| "postproc":{"op":"concat","pad":""} | ||
| }, | ||
| "default":"salmon_quant/cmd_info.json" | ||
| }, | ||
| { | ||
| "id":"zip_target", | ||
| "required":"no", | ||
| "subst_constructor":{ | ||
| "vals":[ {"subst":"outdatadir"}, "/", {"subst":"rpt"}, ".salmon_quant.zip" ], | ||
| "postproc":{"op":"concat","pad":""} | ||
| } | ||
| }, | ||
| { | ||
| "id":"gene_mapping_flag", | ||
| "required":"no", | ||
| "subst_constructor":{ | ||
| "vals":[ "--geneMap=", {"subst":"annotation_val"} ], | ||
| "postproc":{"op":"concat","pad":""} | ||
| } | ||
| }, | ||
| { | ||
| "id":"salmon_transcriptome_val", | ||
| "required":"yes" | ||
| } | ||
| ], | ||
| "nodes":[ | ||
| { | ||
| "id":"salmon", | ||
| "type":"EXEC", | ||
| "use_STDIN": false, | ||
| "use_STDOUT": true, | ||
| "cmd":[ | ||
| "salmon", | ||
| "--no-version-check", | ||
| "quant", | ||
| "--index", {"subst":"salmon_transcriptome_val"}, | ||
| "--libType", "A", | ||
| "--mates1", "__FQ1_IN__", | ||
| "--mates2", "__FQ2_IN__", | ||
| {"subst":"gene_mapping_flag"}, | ||
| {"subst":"b2c_mt", "ifnull":{"subst_constructor":{ "vals":[ "-p", {"subst":"b2c_mt_val"} ]}}}, | ||
| "--output", {"subst":"salmon_out"} | ||
| ] | ||
| }, | ||
| { | ||
| "id":"zip_salmon_quant", | ||
| "type":"EXEC", | ||
| "use_STDIN": true, | ||
| "use_STDOUT": false, | ||
| "cmd":[ | ||
| "zip", "-r", | ||
| {"subst":"zip_target"}, | ||
| {"subst":"quant"}, | ||
| {"subst":"quant_genes"}, | ||
| {"subst":"lib_format_counts"}, | ||
| {"subst":"libparams"}, | ||
| {"subst":"cmd_info"} | ||
| ] | ||
| } | ||
| ], | ||
| "edges":[ | ||
| { "id":"salmon_to_zip_salmon_quant", "from":"salmon", "to":"zip_salmon_quant"} | ||
| ] | ||
| } |
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