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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,50 +1,58 @@ | ||
| version 1.0 | ||
|
|
||
| #ENCODE DCC RNA-Seq pipeline merge-annotation | ||
| #Maintainer: Otto Jolanki | ||
| #CAPER docker quay.io/encode-dcc/rna-seq-pipeline:v1.1 | ||
| #CAPER singularity docker://quay.io/encode-dcc/rna-seq-pipeline:v1.1 | ||
| #CAPER docker quay.io/encode-dcc/rna-seq-pipeline:v1.2.0 | ||
| #CAPER singularity docker://quay.io/encode-dcc/rna-seq-pipeline:v1.2.0 | ||
| workflow merge_anno { | ||
| # input filenames | ||
| File annotation | ||
| File tRNA | ||
| File spikeins | ||
| # output filename | ||
| String output_filename | ||
| Int? cpu | ||
| Int? memGB | ||
| String? disks | ||
| meta { | ||
| author: "Otto Jolanki" | ||
| version: "v1.2.0" | ||
| } | ||
|
|
||
| input { | ||
| File annotation | ||
| File tRNA | ||
| File spikeins | ||
| String output_filename | ||
| Int? cpu | ||
| Int? memGB | ||
| String? disks | ||
| } | ||
|
|
||
| call merge_annotation { input : | ||
| annotation = annotation, | ||
| tRNA = tRNA, | ||
| spikeins = spikeins, | ||
| output_filename = output_filename, | ||
| annotation=annotation, | ||
| tRNA=tRNA, | ||
| spikeins=spikeins, | ||
| output_filename=output_filename, | ||
| } | ||
| } | ||
| task merge_annotation { | ||
| File annotation | ||
| File tRNA | ||
| File spikeins | ||
| String output_filename | ||
| Int? cpu | ||
| Int? memGB | ||
| String? disks | ||
| input { | ||
| File annotation | ||
| File tRNA | ||
| File spikeins | ||
| String output_filename | ||
| Int? cpu | ||
| Int? memGB | ||
| String? disks | ||
| } | ||
|
|
||
| command { | ||
| python3 $(which merge_annotation.py) \ | ||
| ${"--annotation " + annotation} \ | ||
| ${"--tRNA " + tRNA} \ | ||
| ${"--spikeins " + spikeins} \ | ||
| ${"--output_filename " + output_filename} | ||
| ~{"--annotation " + annotation} \ | ||
| ~{"--tRNA " + tRNA} \ | ||
| ~{"--spikeins " + spikeins} \ | ||
| ~{"--output_filename " + output_filename} | ||
| } | ||
| output { | ||
| File merged_annotation = glob("${output_filename}")[0] | ||
| File merged_annotation = output_filename | ||
| } | ||
| runtime { | ||
| cpu : select_first([cpu,2]) | ||
| memory : "${select_first([memGB,'8'])} GB" | ||
| memory : "~{select_first([memGB,'8'])} GB" | ||
| disks : select_first([disks,"local-disk 100 SSD"]) | ||
| } | ||
| } |
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