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mirpedrolmirpedrol
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Merge pull request #51 from mirpedrol/update-modules-msa-treealign
add more module to msa_treealign
2 parents 47da7ae + bd2cf26 commit 3c0a94d

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7 files changed

+161
-3
lines changed

7 files changed

+161
-3
lines changed

‎classes/msa_treealign.yml‎

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@@ -52,6 +52,8 @@ components:
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- famsa/align
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- magus/align
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- tcoffee/align
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- tcoffee/regressive
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- upp/align
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testdata:
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- - "[ id:'test' ]"
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- "file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true)"

‎subworkflows/mirpedrol/msa_treealign/main.nf‎

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@@ -2,6 +2,8 @@ include { CLUSTALO_ALIGN } from '../../../modules/nf-core/clustalo/align/main'
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include { FAMSA_ALIGN } from '../../../modules/nf-core/famsa/align/main'
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include { MAGUS_ALIGN } from '../../../modules/nf-core/magus/align/main'
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include { TCOFFEE_ALIGN } from '../../../modules/nf-core/tcoffee/align/main'
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include { TCOFFEE_REGRESSIVE } from '../../../modules/nf-core/tcoffee/regressive/main'
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include { UPP_ALIGN } from '../../../modules/nf-core/upp/align/main'
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workflow MSA_TREEALIGN {
@@ -25,6 +27,10 @@ workflow MSA_TREEALIGN {
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return [ meta, fasta ]
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tcoffee_align: tool == "tcoffee_align"
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return [ meta, fasta ]
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tcoffee_regressive: tool == "tcoffee_regressive"
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return [ meta, fasta ]
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upp_align: tool == "upp_align"
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return [ meta, fasta ]
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}
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.set { ch_fasta_branch }
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ch_tree
@@ -38,6 +44,10 @@ workflow MSA_TREEALIGN {
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return [ meta, tree ]
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tcoffee_align: tool == "tcoffee_align"
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return [ meta, tree ]
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tcoffee_regressive: tool == "tcoffee_regressive"
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return [ meta, tree ]
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upp_align: tool == "upp_align"
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return [ meta, tree ]
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}
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.set { ch_tree_branch }
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@@ -57,6 +67,14 @@ workflow MSA_TREEALIGN {
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ch_out_alignment = ch_out_alignment.mix(TCOFFEE_ALIGN.out.alignment)
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ch_out_versions = ch_out_versions.mix(TCOFFEE_ALIGN.out.versions)
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TCOFFEE_REGRESSIVE( ch_fasta_branch.tcoffee_regressive, ch_tree_branch.tcoffee_regressive, [[], [], []], [] )
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ch_out_alignment = ch_out_alignment.mix(TCOFFEE_REGRESSIVE.out.alignment)
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ch_out_versions = ch_out_versions.mix(TCOFFEE_REGRESSIVE.out.versions)
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UPP_ALIGN( ch_fasta_branch.upp_align, ch_tree_branch.upp_align, [] )
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ch_out_alignment = ch_out_alignment.mix(UPP_ALIGN.out.alignment)
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ch_out_versions = ch_out_versions.mix(UPP_ALIGN.out.versions)
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emit:

‎subworkflows/mirpedrol/msa_treealign/meta.yml‎

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@@ -11,6 +11,10 @@ components:
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git_remote: "https://github.com/nf-core/modules.git"
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- tcoffee/align:
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git_remote: "https://github.com/nf-core/modules.git"
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- tcoffee/regressive:
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git_remote: "https://github.com/nf-core/modules.git"
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- upp/align:
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git_remote: "https://github.com/nf-core/modules.git"
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input:
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- ch_fasta:

‎subworkflows/mirpedrol/msa_treealign/msa_treealign.diff‎

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@@ -0,0 +1,19 @@
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Changes in component 'mirpedrol/msa_treealign'
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'subworkflows/mirpedrol/msa_treealign/.nf-test.log' was created
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'subworkflows/mirpedrol/msa_treealign/meta.yml' is unchanged
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'subworkflows/mirpedrol/msa_treealign/main.nf' is unchanged
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'subworkflows/mirpedrol/msa_treealign/tests/main.nf.test.snap' was created
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'subworkflows/mirpedrol/msa_treealign/tests/nextflow.config' was created
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Changes in 'msa_treealign/tests/main.nf.test':
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--- subworkflows/mirpedrol/msa_treealign/tests/main.nf.test
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+++ subworkflows/mirpedrol/msa_treealign/tests/main.nf.test
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@@ -111,6 +111,7 @@
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}
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test("upp/align") {
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+ config "./nextflow.config"
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when {
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workflow {
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************************************************************

‎subworkflows/mirpedrol/msa_treealign/tests/main.nf.test‎

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Original file line numberDiff line numberDiff line change
@@ -11,6 +11,8 @@ nextflow_workflow {
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tag "subworkflows/../../modules/nf-core/famsa/align"
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tag "subworkflows/../../modules/nf-core/magus/align"
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tag "subworkflows/../../modules/nf-core/tcoffee/align"
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tag "subworkflows/../../modules/nf-core/tcoffee/regressive"
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tag "subworkflows/../../modules/nf-core/upp/align"
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test("clustalo/align") {
@@ -89,5 +91,44 @@ nextflow_workflow {
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}
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}
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94+
test("tcoffee/regressive") {
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when {
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workflow {
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"""
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input[0] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true), 'tcoffee_regressive'] )
100+
input[1] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.dnd', checkIfExists: true), 'tcoffee_regressive'] )
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"""
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}
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}
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then {
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assertAll(
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{ assert workflow.success },
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{ assert snapshot(workflow.out).match("tcoffee/regressive") },
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)
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}
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}
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test("upp/align") {
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config "./nextflow.config"
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when {
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workflow {
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"""
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input[0] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.aln', checkIfExists: true), 'upp_align'] )
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input[1] = Channel.of( [[ id:'test' ], file(params.modules_testdata_base_path + 'genomics/eukaryotes/anemonia_sulcata/seatoxin-ref.dnd', checkIfExists: true), 'upp_align'] )
121+
"""
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}
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}
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then {
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assertAll(
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{ assert workflow.success },
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{ assert snapshot(workflow.out).match("upp/align") },
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)
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}
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}
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}

‎subworkflows/mirpedrol/msa_treealign/tests/main.nf.test.snap‎

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@@ -44,7 +44,7 @@
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]
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],
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"1": [
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"versions.yml:md5,dc23c65f66a62f337556459f11efb7b3"
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"versions.yml:md5,a1ee55248052d51e7dea2c7ae59d27d7"
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],
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"alignment": [
5050
[
@@ -55,7 +55,7 @@
5555
]
5656
],
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"versions": [
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"versions.yml:md5,dc23c65f66a62f337556459f11efb7b3"
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"versions.yml:md5,a1ee55248052d51e7dea2c7ae59d27d7"
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]
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}
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],
@@ -65,6 +65,40 @@
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},
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"timestamp": "2025-08-01T14:08:10.972913645"
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},
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"tcoffee/regressive": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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"test.aln:md5,a399645e1b14b858ccc9aef57ce3d9f8"
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]
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],
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"1": [
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"versions.yml:md5,167b47da97b1e1b8f168aa85495245b4"
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],
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"alignment": [
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[
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{
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"id": "test"
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},
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"test.aln:md5,a399645e1b14b858ccc9aef57ce3d9f8"
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]
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],
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"versions": [
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"versions.yml:md5,167b47da97b1e1b8f168aa85495245b4"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-11-26T14:48:00.884458852"
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},
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"magus/align": {
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"content": [
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{
@@ -130,5 +164,38 @@
130164
"nextflow": "25.04.6"
131165
},
132166
"timestamp": "2025-08-01T14:09:48.216260207"
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},
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"upp/align": {
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"content": [
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{
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"0": [
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[
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{
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"id": "test"
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},
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"test.aln:md5,a543b6c4d215628c0307111268496557"
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]
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],
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"1": [
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"versions.yml:md5,480e12b84ba1a750dc9e347a0ee77d1b"
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],
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"alignment": [
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[
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{
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"id": "test"
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},
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"test.aln:md5,a543b6c4d215628c0307111268496557"
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]
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],
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"versions": [
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"versions.yml:md5,480e12b84ba1a750dc9e347a0ee77d1b"
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]
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}
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],
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"meta": {
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"nf-test": "0.9.2",
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"nextflow": "25.10.0"
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},
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"timestamp": "2025-11-26T14:48:08.969096652"
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}
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}
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}

‎subworkflows/mirpedrol/msa_treealign/tests/nextflow.config‎

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@@ -0,0 +1,7 @@
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process {
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withName: "UPP_ALIGN" {
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ext.args = { "-m amino" }
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}
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}

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