diff --git a/validate-seqtools/main.nf b/validate-seqtools/main.nf index 0d86420..b4dccd0 100755 --- a/validate-seqtools/main.nf +++ b/validate-seqtools/main.nf @@ -24,7 +24,7 @@ /* this block is auto-generated based on info from pkg.json where */ /* changes can be made if needed, do NOT modify this block manually */ nextflow.enable.dsl = 2 -version = '0.1.0' // package version +version = '0.1.1' container = [ 'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools' @@ -67,10 +67,13 @@ process validateSeqtools { // add and initialize variables here as needed args_skip_md5sum_check = params.skip_md5sum_check ? "--skip_md5sum_check " : "" """ + cp ${json_file} local_copy python3 /tools/main.py \ - -j ${json_file} \ + -j local_copy \ ${args_skip_md5sum_check} \ > seq-tools.log 2>&1 + rm local_copy + ls validation_report.PASS*.jsonl && ( exit 0 || exit 1) """ } diff --git a/validate-seqtools/pkg.json b/validate-seqtools/pkg.json index 89de3e3..c4f3211 100644 --- a/validate-seqtools/pkg.json +++ b/validate-seqtools/pkg.json @@ -1,6 +1,6 @@ { "name": "validate-seqtools", - "version": "0.1.0", + "version": "0.1.1", "description": "Using Seq-tools, validates molecular", "main": "main.nf", "deprecated": false, diff --git a/validate-seqtools/tests/checker.nf b/validate-seqtools/tests/checker.nf index 5db58b2..cffb8e3 100755 --- a/validate-seqtools/tests/checker.nf +++ b/validate-seqtools/tests/checker.nf @@ -29,7 +29,7 @@ /* this block is auto-generated based on info from pkg.json where */ /* changes can be made if needed, do NOT modify this block manually */ nextflow.enable.dsl = 2 -version = '0.1.0' // package version +version = '0.1.1' container = [ 'ghcr.io': 'ghcr.io/icgc-argo/argo-data-submission.validate-seqtools' diff --git a/validate-seqtools/tests/test-job-fq.json b/validate-seqtools/tests/local-test-job-fq.json similarity index 100% rename from validate-seqtools/tests/test-job-fq.json rename to validate-seqtools/tests/local-test-job-fq.json