From 50c5e43551ace3dfdfee3e9db8a8549939b758c8 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Thu, 19 Sep 2024 14:43:40 +0200 Subject: [PATCH 1/7] Warning when kalign fails with error 132 --- CHANGELOG.md | 1 + conf/modules.config | 8 ++++++++ 2 files changed, 9 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ac0f2ae3..3f08a9e2 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. +- [[#151](https://github.com/nf-core/multiplesequencealign/pull/151)] - Ignore kalign error 132 and print a warning (incompatibility with some CPU types). ### `Dependencies` diff --git a/conf/modules.config b/conf/modules.config index 0fdc9259..1c89eda2 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -142,6 +142,14 @@ } } + withName: "KALIGN_ALIGN" { + errorStrategy { + if (task.exitStatus == 132) { + log.warn "KALIGN failed because is incompatible with some CPU types - error will be ignored." + return 'ignore' + } + } + withName: "MTMALIGN_ALIGN" { tag = { [ From 9a43121725d969b9891cd154584e2d48772eed56 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Thu, 19 Sep 2024 14:46:22 +0200 Subject: [PATCH 2/7] Fix tyop --- conf/modules.config | 1 + 1 file changed, 1 insertion(+) diff --git a/conf/modules.config b/conf/modules.config index 1c89eda2..965fb777 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -147,6 +147,7 @@ if (task.exitStatus == 132) { log.warn "KALIGN failed because is incompatible with some CPU types - error will be ignored." return 'ignore' + } } } From 6f3ae62feb4f3f31cfb78309f94734e0b0b3ae86 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Thu, 19 Sep 2024 15:07:22 +0200 Subject: [PATCH 3/7] Another tyop --- conf/modules.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules.config b/conf/modules.config index 965fb777..f6be50ac 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -143,7 +143,7 @@ } withName: "KALIGN_ALIGN" { - errorStrategy { + errorStrategy = { if (task.exitStatus == 132) { log.warn "KALIGN failed because is incompatible with some CPU types - error will be ignored." return 'ignore' From a09a80fe62656bd6734fcfe8c3298515f0ad55ea Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Thu, 19 Sep 2024 15:28:22 +0200 Subject: [PATCH 4/7] Include errorStrategy in module instead of modules.config --- conf/modules.config | 9 --------- modules/nf-core/kalign/align/main.nf | 7 +++++++ 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index f6be50ac..0fdc9259 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -142,15 +142,6 @@ } } - withName: "KALIGN_ALIGN" { - errorStrategy = { - if (task.exitStatus == 132) { - log.warn "KALIGN failed because is incompatible with some CPU types - error will be ignored." - return 'ignore' - } - } - } - withName: "MTMALIGN_ALIGN" { tag = { [ 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) From 957fc58ba9e1d8cad5c6677fb5726ca031be808c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Thu, 19 Sep 2024 15:38:30 +0200 Subject: [PATCH 5/7] Patch kalign/align module --- modules.json | 115 +++++++++++++----- .../nf-core/kalign/align/kalign-align.diff | 25 ++++ 2 files changed, 111 insertions(+), 29 deletions(-) create mode 100644 modules/nf-core/kalign/align/kalign-align.diff diff --git a/modules.json b/modules.json index 46f8b5c3..ee9d9da0 100644 --- a/modules.json +++ b/modules.json @@ -8,128 +8,179 @@ "clustalo/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "clustalo/guidetree": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "csvtk/concat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "csvtk/join": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/csvtk/join/csvtk-join.diff" }, "famsa/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "famsa/guidetree": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "foldmason/easymsa": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "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", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mafft": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "magus/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "magus/guidetree": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mtmalign/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "muscle5/super5": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "pigz/compress": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "pigz/uncompress": { "branch": "master", "git_sha": "c00055a0b13d622b4f1f51a8e5be31deaf99ded7", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tcoffee/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tcoffee/alncompare": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tcoffee/consensus": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tcoffee/irmsd": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tcoffee/seqreformat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tcoffee/tcs": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "untar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "upp/align": { "branch": "master", "git_sha": "3be751e610b332efd94c2e82ddab5b5c65cfe852", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -138,20 +189,26 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file 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 +************************************************************ From 036d0c0b6ab6b31aa99f1f8f2abee23077d495f4 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Thu, 19 Sep 2024 15:39:32 +0200 Subject: [PATCH 6/7] Fix PR number in changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3f08a9e2..538f6d18 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -49,7 +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. -- [[#151](https://github.com/nf-core/multiplesequencealign/pull/151)] - Ignore kalign error 132 and print a warning (incompatibility with some CPU types). +- [[#152](https://github.com/nf-core/multiplesequencealign/pull/152)] - Ignore kalign error 132 and print a warning (incompatibility with some CPU types). ### `Dependencies` From 64a0eda3f0f1adf54c32945be11d80eb0d8b194d Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Thu, 19 Sep 2024 13:44:39 +0000 Subject: [PATCH 7/7] fix prettier --- modules.json | 114 +++++++++++++-------------------------------------- 1 file changed, 29 insertions(+), 85 deletions(-) diff --git a/modules.json b/modules.json index ee9d9da0..3b08d041 100644 --- a/modules.json +++ b/modules.json @@ -8,179 +8,129 @@ "clustalo/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "clustalo/guidetree": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "csvtk/concat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "csvtk/join": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/csvtk/join/csvtk-join.diff" }, "famsa/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "famsa/guidetree": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "foldmason/easymsa": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "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", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mafft": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "magus/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "magus/guidetree": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mtmalign/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "muscle5/super5": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "pigz/compress": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "pigz/uncompress": { "branch": "master", "git_sha": "c00055a0b13d622b4f1f51a8e5be31deaf99ded7", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/align": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/alncompare": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/consensus": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/irmsd": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/seqreformat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tcoffee/tcs": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "untar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "upp/align": { "branch": "master", "git_sha": "3be751e610b332efd94c2e82ddab5b5c65cfe852", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -189,26 +139,20 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +}