From 63b1fdcc786974634347f5585af19ea57f896b1a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Tue, 19 Aug 2025 15:57:23 +0200 Subject: [PATCH 1/6] add mafft/align module to msa_alignment class --- classes/msa_alignment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/classes/msa_alignment.yml b/classes/msa_alignment.yml index 4629db1..fb9ef51 100644 --- a/classes/msa_alignment.yml +++ b/classes/msa_alignment.yml @@ -43,7 +43,7 @@ components: - famsa/align - kalign/align - learnmsa/align - #- mafft/align # Multiple inputs - to fix upstream + - mafft/align # Multiple inputs - magus/align - muscle5/super5 - tcoffee/align # Needs an argument to return the alignment in fasta From c80952c1e76bb1eba941995484dcee5a5c569404 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 20 Aug 2025 14:45:36 +0000 Subject: [PATCH 2/6] [automated] Update expanded subworkflows for class msa_alignment --- subworkflows/mirpedrol/msa_alignment/main.nf | 7 +++++++ subworkflows/mirpedrol/msa_alignment/meta.yml | 2 ++ .../msa_alignment/tests/main.nf.test | 19 +++++++++++++++++++ 3 files changed, 28 insertions(+) diff --git a/subworkflows/mirpedrol/msa_alignment/main.nf b/subworkflows/mirpedrol/msa_alignment/main.nf index 0f21560..82e8978 100644 --- a/subworkflows/mirpedrol/msa_alignment/main.nf +++ b/subworkflows/mirpedrol/msa_alignment/main.nf @@ -2,6 +2,7 @@ include { CLUSTALO_ALIGN } from '../../../modules/nf-core/clustalo/align/main' include { FAMSA_ALIGN } from '../../../modules/nf-core/famsa/align/main' include { KALIGN_ALIGN } from '../../../modules/nf-core/kalign/align/main' include { LEARNMSA_ALIGN } from '../../../modules/nf-core/learnmsa/align/main' +include { MAFFT_ALIGN } from '../../../modules/nf-core/mafft/align/main' include { MAGUS_ALIGN } from '../../../modules/nf-core/magus/align/main' include { MUSCLE5_SUPER5 } from '../../../modules/nf-core/muscle5/super5/main' include { TCOFFEE_ALIGN } from '../../../modules/nf-core/tcoffee/align/main' @@ -27,6 +28,8 @@ workflow MSA_ALIGNMENT { return [ meta, fasta ] learnmsa_align: tool == "learnmsa_align" return [ meta, fasta ] + mafft_align: tool == "mafft_align" + return [ meta, fasta ] magus_align: tool == "magus_align" return [ meta, fasta ] muscle5_super5: tool == "muscle5_super5" @@ -52,6 +55,10 @@ workflow MSA_ALIGNMENT { ch_out_alignment = ch_out_alignment.mix(LEARNMSA_ALIGN.out.alignment) ch_out_versions = ch_out_versions.mix(LEARNMSA_ALIGN.out.versions) + MAFFT_ALIGN( ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, [] ) + ch_out_alignment = ch_out_alignment.mix(MAFFT_ALIGN.out.fas) + ch_out_versions = ch_out_versions.mix(MAFFT_ALIGN.out.versions) + MAGUS_ALIGN( ch_fasta_branch.magus_align, [[], []], [] ) ch_out_alignment = ch_out_alignment.mix(MAGUS_ALIGN.out.alignment) ch_out_versions = ch_out_versions.mix(MAGUS_ALIGN.out.versions) diff --git a/subworkflows/mirpedrol/msa_alignment/meta.yml b/subworkflows/mirpedrol/msa_alignment/meta.yml index 4f5d7f3..4a3f42a 100644 --- a/subworkflows/mirpedrol/msa_alignment/meta.yml +++ b/subworkflows/mirpedrol/msa_alignment/meta.yml @@ -11,6 +11,8 @@ components: git_remote: "https://github.com/nf-core/modules.git" - learnmsa/align: git_remote: "https://github.com/nf-core/modules.git" + - mafft/align: + git_remote: "https://github.com/nf-core/modules.git" - magus/align: git_remote: "https://github.com/nf-core/modules.git" - muscle5/super5: diff --git a/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test b/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test index 720acb7..a6b9a4c 100644 --- a/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test +++ b/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test @@ -11,6 +11,7 @@ nextflow_workflow { tag "subworkflows/../../modules/nf-core/famsa/align" tag "subworkflows/../../modules/nf-core/kalign/align" tag "subworkflows/../../modules/nf-core/learnmsa/align" + tag "subworkflows/../../modules/nf-core/mafft/align" tag "subworkflows/../../modules/nf-core/magus/align" tag "subworkflows/../../modules/nf-core/muscle5/super5" tag "subworkflows/../../modules/nf-core/tcoffee/align" @@ -90,6 +91,24 @@ nextflow_workflow { } } + test("mafft/align") { + + when { + workflow { + """ + input[0] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true), 'mafft_align'] ) + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match("mafft/align") }, + ) + } + } + test("magus/align") { when { From 0c3321f6294834fb268589763fd50f28723b4339 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" Date: Wed, 20 Aug 2025 14:50:18 +0000 Subject: [PATCH 3/6] [automated] Update subworkflows msa_alignment snapshot --- .../msa_alignment/tests/main.nf.test.snap | 25 ++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap b/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap index 7ec9c2a..4f5c45c 100644 --- a/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap +++ b/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap @@ -131,6 +131,29 @@ }, "timestamp": "2025-08-01T07:01:54.454247483" }, + "mafft/align": { + "content": [ + { + "0": [ + + ], + "1": [ + + ], + "alignment": [ + + ], + "versions": [ + + ] + } + ], + "meta": { + "nf-test": "0.9.2", + "nextflow": "25.04.6" + }, + "timestamp": "2025-08-20T14:48:11.902561829" + }, "magus/align": { "content": [ [ @@ -209,4 +232,4 @@ }, "timestamp": "2025-08-01T07:27:07.276478754" } -} +} \ No newline at end of file From 4d811a5f68c81e942b44bb280bfe9603fa349d0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 20 Aug 2025 17:13:29 +0200 Subject: [PATCH 4/6] fix mafft/align input channels --- subworkflows/mirpedrol/msa_alignment/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/mirpedrol/msa_alignment/main.nf b/subworkflows/mirpedrol/msa_alignment/main.nf index 82e8978..1619385 100644 --- a/subworkflows/mirpedrol/msa_alignment/main.nf +++ b/subworkflows/mirpedrol/msa_alignment/main.nf @@ -55,7 +55,7 @@ workflow MSA_ALIGNMENT { ch_out_alignment = ch_out_alignment.mix(LEARNMSA_ALIGN.out.alignment) ch_out_versions = ch_out_versions.mix(LEARNMSA_ALIGN.out.versions) - MAFFT_ALIGN( ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, [] ) + MAFFT_ALIGN( ch_fasta_branch.mafft_align, [[], []], [[], []], [[], []], [[], []], [[], []], [] ) ch_out_alignment = ch_out_alignment.mix(MAFFT_ALIGN.out.fas) ch_out_versions = ch_out_versions.mix(MAFFT_ALIGN.out.versions) From 9d1feebc19695811b02e4d90fd7d0f88980e68fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 20 Aug 2025 17:25:36 +0200 Subject: [PATCH 5/6] update mafft/align snapshot --- .../msa_alignment/tests/main.nf.test.snap | 20 ++++++++++++++----- 1 file changed, 15 insertions(+), 5 deletions(-) diff --git a/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap b/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap index 4f5c45c..f7e6802 100644 --- a/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap +++ b/subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap @@ -135,16 +135,26 @@ "content": [ { "0": [ - + [ + { + "id": "test" + }, + "test.fas:md5,d443a4d46c7d85f5ea5f5f73148c6f34" + ] ], "1": [ - + "versions.yml:md5,4eac1bd98ea7280bd9822cc13631b619" ], "alignment": [ - + [ + { + "id": "test" + }, + "test.fas:md5,d443a4d46c7d85f5ea5f5f73148c6f34" + ] ], "versions": [ - + "versions.yml:md5,4eac1bd98ea7280bd9822cc13631b619" ] } ], @@ -232,4 +242,4 @@ }, "timestamp": "2025-08-01T07:27:07.276478754" } -} \ No newline at end of file +} From 2eb5986c8719dbd41eec52ffe17291a4451cf92b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 22 Aug 2025 12:17:43 +0200 Subject: [PATCH 6/6] patch msa_alignment --- .../msa_alignment/msa_alignment.diff | 32 +++++++++++++------ 1 file changed, 22 insertions(+), 10 deletions(-) diff --git a/subworkflows/mirpedrol/msa_alignment/msa_alignment.diff b/subworkflows/mirpedrol/msa_alignment/msa_alignment.diff index b17f15c..81e666b 100644 --- a/subworkflows/mirpedrol/msa_alignment/msa_alignment.diff +++ b/subworkflows/mirpedrol/msa_alignment/msa_alignment.diff @@ -1,30 +1,42 @@ Changes in component 'mirpedrol/msa_alignment' 'subworkflows/mirpedrol/msa_alignment/meta.yml' is unchanged -'subworkflows/mirpedrol/msa_alignment/main.nf' is unchanged +Changes in 'msa_alignment/main.nf': +--- subworkflows/mirpedrol/msa_alignment/main.nf ++++ subworkflows/mirpedrol/msa_alignment/main.nf +@@ -55,7 +55,7 @@ + ch_out_alignment = ch_out_alignment.mix(LEARNMSA_ALIGN.out.alignment) + ch_out_versions = ch_out_versions.mix(LEARNMSA_ALIGN.out.versions) + +- MAFFT_ALIGN( ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, ch_fasta_branch.mafft_align, [] ) ++ MAFFT_ALIGN( ch_fasta_branch.mafft_align, [[], []], [[], []], [[], []], [[], []], [[], []], [] ) + ch_out_alignment = ch_out_alignment.mix(MAFFT_ALIGN.out.fas) + ch_out_versions = ch_out_versions.mix(MAFFT_ALIGN.out.versions) + + 'subworkflows/mirpedrol/msa_alignment/tests/main.nf.test.snap' was created 'subworkflows/mirpedrol/msa_alignment/tests/nextflow.config' was created Changes in 'msa_alignment/tests/main.nf.test': --- subworkflows/mirpedrol/msa_alignment/tests/main.nf.test +++ subworkflows/mirpedrol/msa_alignment/tests/main.nf.test -@@ -15,6 +15,7 @@ +@@ -16,6 +16,7 @@ tag "subworkflows/../../modules/nf-core/muscle5/super5" tag "subworkflows/../../modules/nf-core/tcoffee/align" - + + config './nextflow.config' - + test("clustalo/align") { - -@@ -70,7 +71,8 @@ + +@@ -71,7 +72,8 @@ } } - + - test("learnmsa/align") { + test("learnmsa/align - stub") { + options "-stub" - + when { workflow { -@@ -83,7 +85,7 @@ +@@ -84,7 +86,7 @@ then { assertAll( { assert workflow.success }, @@ -33,7 +45,7 @@ Changes in 'msa_alignment/tests/main.nf.test': ) } } -@@ -101,7 +103,12 @@ +@@ -120,7 +122,12 @@ then { assertAll( { assert workflow.success },