kfukuta/wf-transcriptomes-v202
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge branch 'use-ruo-template' into 'dev'

Browse Source 
Pin wf-template@ruo-next

See merge request epi2melabs/workflows/wf-transcriptomes!276
This commit is contained in:
Natalia Garcia 2026-05-19 14:03:14 +00:00
commit c54ba7b0d7
2 changed files with 2 additions and 2 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
.gitlab-ci.yml
View File

@ -16,7 +16,7 @@ variables:
PYTEST_TESTS_PATH: "bin/workflow_glue/tests/common"
RTEST_CONTAINER_NAME: "wf-transcriptomes-core"
RTEST_CONTAINER_CONFIG_KEY: "container_sha"
WF_TEMPLATE_ENFORCEMENT_BRANCH: "CW-6552"
WF_TEMPLATE_ENFORCEMENT_BRANCH: "ruo-next"
pytest_wfcontainer:
extends: pytest

2
lib/common.nf
View File

@ -81,7 +81,7 @@ process minimap2_alignment {
emit: alignment
script:
String reset_cmd_body = "samtools reset -x tp,cm,s1,s2,NM,MD,AS,SA,ms,nn,ts,cg,cs,dv,de,rl"
String fastq_cmd_body = "samtools fastq -T *"
String fastq_cmd_body = "samtools fastq -T '*'"
// Default required threads is 6
// Samtools x3 and bamstats will all be single threaded
def minimap2_threads = Math.max(task.cpus - 4 , 1)