diff --git a/CHANGELOG.md b/CHANGELOG.md index ac0f2ae3..538f6d18 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -49,6 +49,7 @@ Initial release of nf-core/multiplesequencealign, created with the [nf-core](htt - [[#111](https://github.com/nf-core/multiplesequencealign/pull/111)] - Fix linting warnings (mostly versions). - [[#134](https://github.com/nf-core/multiplesequencealign/pull/134)] - Code revision for release preparation. - [[#138](https://github.com/nf-core/multiplesequencealign/pull/138)] - MultiQC as nf-core module and fix visualization. +- [[#152](https://github.com/nf-core/multiplesequencealign/pull/152)] - Ignore kalign error 132 and print a warning (incompatibility with some CPU types). ### `Dependencies` diff --git a/modules.json b/modules.json index 46f8b5c3..3b08d041 100644 --- a/modules.json +++ b/modules.json @@ -44,7 +44,8 @@ "kalign/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": ["modules"], + "patch": "modules/nf-core/kalign/align/kalign-align.diff" }, "learnmsa/align": { "branch": "master", diff --git a/modules/nf-core/kalign/align/kalign-align.diff b/modules/nf-core/kalign/align/kalign-align.diff new file mode 100644 index 00000000..864e7f2c --- /dev/null +++ b/modules/nf-core/kalign/align/kalign-align.diff @@ -0,0 +1,25 @@ +Changes in module 'nf-core/kalign/align' +'modules/nf-core/kalign/align/environment.yml' is unchanged +'modules/nf-core/kalign/align/meta.yml' is unchanged +Changes in 'kalign/align/main.nf': +--- modules/nf-core/kalign/align/main.nf ++++ modules/nf-core/kalign/align/main.nf +@@ -6,6 +6,13 @@ + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-5cd0277547c6b33133225c8ce14c0cf2a4396ea2:0a70b6d89a3e06fbdc4a735461e8b98ff32ee5de-0': + 'biocontainers/mulled-v2-5cd0277547c6b33133225c8ce14c0cf2a4396ea2:0a70b6d89a3e06fbdc4a735461e8b98ff32ee5de-0' }" ++ ++ errorStrategy { ++ if (task.exitStatus == 132) { ++ log.warn "KALIGN failed because is incompatible with some CPU types - error will be ignored." ++ return 'ignore' ++ } ++ } + + input: + tuple val(meta), path(fasta) + +'modules/nf-core/kalign/align/tests/main.nf.test.snap' is unchanged +'modules/nf-core/kalign/align/tests/tags.yml' is unchanged +'modules/nf-core/kalign/align/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/kalign/align/main.nf b/modules/nf-core/kalign/align/main.nf index e1601e15..e9c3442f 100644 --- a/modules/nf-core/kalign/align/main.nf +++ b/modules/nf-core/kalign/align/main.nf @@ -7,6 +7,13 @@ process KALIGN_ALIGN { 'https://depot.galaxyproject.org/singularity/mulled-v2-5cd0277547c6b33133225c8ce14c0cf2a4396ea2:0a70b6d89a3e06fbdc4a735461e8b98ff32ee5de-0': 'biocontainers/mulled-v2-5cd0277547c6b33133225c8ce14c0cf2a4396ea2:0a70b6d89a3e06fbdc4a735461e8b98ff32ee5de-0' }" + errorStrategy { + if (task.exitStatus == 132) { + log.warn "KALIGN failed because is incompatible with some CPU types - error will be ignored." + return 'ignore' + } + } + input: tuple val(meta), path(fasta) val(compress)