Entering edit mode
9.3 years ago
bryan.cosca
•
0
I'm working on a CWL v1.0 workflow that copies a header file to a bunch of .sam files.
In bash, it would look like this:
cat chromosome_list.txt | parallel cp wg19header.txt sample_name.{}.sam
In CWL, I'm a little confused on how to copy files, and where inputs and outputs go. For example, my code is:
scatter-wf1.cwl
#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
inputs:
chr_chrom: string[] #try array of files, see scatter-clt-copies-to-foo.txt.cwl
wg_19_header: File
outputs: []
requirements:
- class: ScatterFeatureRequirement
steps:
step1:
in:
chroms: chr_chrom
header: wg_19_header
out: []
scatter: chroms
run:
class: CommandLineTool
inputs:
chroms:
type: string
inputBinding:
position: 1
header:
type: File
inputBinding:
position: 0
outputs: []
baseCommand: "cp"
wf.json
"chr_chrom": ["chr1","chr10","chr11","chr12","chr13",
"chr14","chr15","chr16","chr17","chr18",
"chr19","chr2","chr20","chr21","chr22",
"chr3","chr4","chr5","chr6","chr7",
"chr8","chr9","chrM","chrX","chrY"],
"wg_19_header": {
"class":"File",
"path":"WG_19_HEADER.txt"
}
out:
cwl-runner scatter-wf1.cwl wf.json
/usr/local/bin/cwl-runner 1.0.20160712154127
[job step1] /tmp/tmpYeX0Jh$ cp \
/tmp/tmpxfocja/stgda17bec7-cc42-47e4-9b14-43eb5b0d172c/WG_19_HEADER.txt \
chr1
[job step1_2] /tmp/tmpTbkbkg$ cp \
/tmp/tmpZGzuut/stg8eef238b-e8de-4b82-b4c8-f55a24a108a8/WG_19_HEADER.txt \
chr10
[job step1_3] /tmp/tmpqh0zae$ cp \
/tmp/tmp4_ezcO/stgb18ca7d5-a4ce-4aac-9777-ca3f03543d20/WG_19_HEADER.txt \
chr11
[job step1_4] /tmp/tmp8SuQry$ cp \
/tmp/tmpcA4uid/stgdbf26c9c-4e8b-4bff-a0e4-fc0e78cd50a1/WG_19_HEADER.txt \
chr12
[job step1_5] /tmp/tmpe_oKVD$ cp \
/tmp/tmpdig2y9/stg34997f9c-d295-462b-a040-f2f1bcb8427f/WG_19_HEADER.txt \
chr13
[job step1_6] /tmp/tmpxK8Rk4$ cp \
/tmp/tmpHxwzD9/stg3fbef6a9-62c2-43fc-be00-4dd56b0670d9/WG_19_HEADER.txt \
chr14
[job step1_7] /tmp/tmpSYoYvs$ cp \
/tmp/tmpwhopwS/stgfaff69bb-c155-46e2-b26f-cb026b87a0d1/WG_19_HEADER.txt \
chr15
[job step1_8] /tmp/tmprJgGoC$ cp \
/tmp/tmpDB_H1r/stg943d25cd-03b4-45ec-855c-3982d2668718/WG_19_HEADER.txt \
chr16
[job step1_9] /tmp/tmpSDyPBG$ cp \
/tmp/tmpvQOzIv/stgb8add355-b76b-4e5d-8881-5abd3221df07/WG_19_HEADER.txt \
chr17
[job step1_10] /tmp/tmpxVg9Hz$ cp \
/tmp/tmpBdpL6G/stga17012be-d7e2-4598-a9fa-f2def5235588/WG_19_HEADER.txt \
chr18
[job step1_11] /tmp/tmprs0Qvz$ cp \
/tmp/tmpS7qC7L/stgf5c7df94-7c78-4f74-90a8-8c6dedc2996c/WG_19_HEADER.txt \
chr19
[job step1_12] /tmp/tmpqXGm06$ cp \
/tmp/tmpi0ZoMS/stg13a60c8e-728c-426b-9c98-46a2fbf1fef6/WG_19_HEADER.txt \
chr2
[job step1_13] /tmp/tmpVTK4z4$ cp \
/tmp/tmpJ_uOXH/stg6ebd6145-f6a1-4b5f-aa55-8106f10cf04a/WG_19_HEADER.txt \
chr20
[job step1_14] /tmp/tmpDtwARH$ cp \
/tmp/tmpAJTkhx/stg4ca575ae-d993-42f5-a47c-fe7e9db75254/WG_19_HEADER.txt \
chr21
[job step1_15] /tmp/tmpAgE7mT$ cp \
/tmp/tmpvc8lnE/stg55aa1a27-6ee0-416c-ba7d-58a48aa15f5b/WG_19_HEADER.txt \
chr22
[job step1_16] /tmp/tmptGk1kY$ cp \
/tmp/tmpBjH7fu/stgfa446779-b6f3-459c-9079-1bdaf2b2f653/WG_19_HEADER.txt \
chr3
[job step1_17] /tmp/tmpZLm39N$ cp \
/tmp/tmppMNd12/stgeebade44-ce62-4bd5-bd6a-61ea1540ac61/WG_19_HEADER.txt \
chr4
[job step1_18] /tmp/tmpnGGHbj$ cp \
/tmp/tmpnsP5sY/stg74fc6dd1-3ee7-4147-86f5-2e7a5dc9f9da/WG_19_HEADER.txt \
chr5
[job step1_19] /tmp/tmpTIAxLg$ cp \
/tmp/tmpu5qs1Z/stg16277549-13fe-496c-b2c4-e44dcbf198b0/WG_19_HEADER.txt \
chr6
[job step1_20] /tmp/tmpzy1XqG$ cp \
/tmp/tmpOG9F75/stg5e120e4b-0a17-4fe1-83a3-e408f4fbdd10/WG_19_HEADER.txt \
chr7
[job step1_21] /tmp/tmpl6CqyI$ cp \
/tmp/tmpeayL_J/stg085d50d8-c54d-4750-b852-634644fa1252/WG_19_HEADER.txt \
chr8
[job step1_22] /tmp/tmpCSMeuS$ cp \
/tmp/tmpNZnPR2/stg43d46de0-6cc6-4036-9035-6c9b62f677ca/WG_19_HEADER.txt \
chr9
[job step1_23] /tmp/tmpNIxScl$ cp \
/tmp/tmpWXDD2S/stg7b9fec54-8237-4af2-acd2-3d8dd564cf8b/WG_19_HEADER.txt \
chrM
[job step1_24] /tmp/tmp3sGi5v$ cp \
/tmp/tmpsZ_IVh/stg6dc8363f-1882-46b6-b949-51258321c600/WG_19_HEADER.txt \
chrX
[job step1_25] /tmp/tmpwzZrGn$ cp \
/tmp/tmpHwPv1C/stge54fac4d-d9c9-4bd7-9809-38fc6ad0e235/WG_19_HEADER.txt \
chrY
[step step1] completion status is success
[workflow scatter-wf1.cwl] outdir is /tmp/tmp7eIMDc
Final process status is success
{}
What's the best way to accomplish this? Do I need to change the tmp directory to output the sam file? Do I have to make the json an array of files?
