diff --git a/subworkflows/nf-core/fastq_preprocess/main.nf b/subworkflows/nf-core/fastq_preprocess_seqkit/main.nf similarity index 81% rename from subworkflows/nf-core/fastq_preprocess/main.nf rename to subworkflows/nf-core/fastq_preprocess_seqkit/main.nf index 0b6ab8ce5f5c..ce0f4a5ad0d6 100644 --- a/subworkflows/nf-core/fastq_preprocess/main.nf +++ b/subworkflows/nf-core/fastq_preprocess_seqkit/main.nf @@ -3,22 +3,22 @@ include { SEQKIT_SEQ } from '../../../modules/nf-core/seqkit/seq/main include { SEQKIT_REPLACE } from '../../../modules/nf-core/seqkit/replace/main' include { SEQKIT_RMDUP } from '../../../modules/nf-core/seqkit/rmdup/main' -workflow FASTQ_PREPROCESS { +workflow FASTQ_PREPROCESS_SEQKIT { take: - ch_reads // channel: [ val(meta), [ fastq ] ] - skip_seqkit_sana_pair // boolean - skip_seqkit_seq // boolean - skip_seqkit_replace // boolean - skip_seqkit_rmdup // boolean + ch_reads // channel: [ val(meta), [ fastq ] ] + skip_seqkit_sana_pair // boolean + skip_seqkit_seq // boolean + skip_seqkit_replace // boolean + skip_seqkit_rmdup // boolean main: - ch_versions = Channel.empty() + ch_versions = channel.empty() if (!skip_seqkit_sana_pair) { FASTQ_SANITISE_SEQKIT( ch_reads ) - ch_reads = FASTQ_SANITISE_SEQKIT.out.reads - ch_versions = ch_versions.mix(FASTQ_SANITISE_SEQKIT.out.versions.first()) + ch_reads = FASTQ_SANITISE_SEQKIT.out.reads + ch_versions = ch_versions.mix(FASTQ_SANITISE_SEQKIT.out.versions) } // Split paired-end reads and add strandedness to meta @@ -75,7 +75,6 @@ workflow FASTQ_PREPROCESS { } emit: - reads = ch_reads // channel: [ val(meta), [ fastq ] ] - versions = ch_versions // channel: [ versions.yml ] - + reads = ch_reads // channel: [ val(meta), [ fastq ] ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_preprocess/meta.yml b/subworkflows/nf-core/fastq_preprocess_seqkit/meta.yml similarity index 97% rename from subworkflows/nf-core/fastq_preprocess/meta.yml rename to subworkflows/nf-core/fastq_preprocess_seqkit/meta.yml index 8cb30862e321..a3c6eaacbf74 100644 --- a/subworkflows/nf-core/fastq_preprocess/meta.yml +++ b/subworkflows/nf-core/fastq_preprocess_seqkit/meta.yml @@ -1,8 +1,8 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json -name: "fastq_preprocess" +name: "fastq_preprocess_seqkit" description: Subworkflow that preprocesses FASTQ files keywords: - - fasta + - fastq - seqkit - preprocessing components: diff --git a/subworkflows/nf-core/fastq_preprocess/nextflow.config b/subworkflows/nf-core/fastq_preprocess_seqkit/nextflow.config similarity index 99% rename from subworkflows/nf-core/fastq_preprocess/nextflow.config rename to subworkflows/nf-core/fastq_preprocess_seqkit/nextflow.config index 0b0a68dd1d22..4e615588b706 100644 --- a/subworkflows/nf-core/fastq_preprocess/nextflow.config +++ b/subworkflows/nf-core/fastq_preprocess_seqkit/nextflow.config @@ -1,8 +1,6 @@ // IMPORTANT: This config file should be included to ensure that the subworkflow works properly. process { - withName: SEQKIT_SANA { ext.prefix = { "${meta.id}_${meta.strandness}" } } - } diff --git a/subworkflows/nf-core/fastq_preprocess/tests/main.nf.test b/subworkflows/nf-core/fastq_preprocess_seqkit/tests/main.nf.test similarity index 97% rename from subworkflows/nf-core/fastq_preprocess/tests/main.nf.test rename to subworkflows/nf-core/fastq_preprocess_seqkit/tests/main.nf.test index 44104ac2fc53..7b165120fab7 100644 --- a/subworkflows/nf-core/fastq_preprocess/tests/main.nf.test +++ b/subworkflows/nf-core/fastq_preprocess_seqkit/tests/main.nf.test @@ -1,14 +1,14 @@ nextflow_workflow { - name "Test Subworkflow FASTQ_PREPROCESS" + name "Test Subworkflow FASTQ_PREPROCESS_SEQKIT" script "../main.nf" - workflow "FASTQ_PREPROCESS" + workflow "FASTQ_PREPROCESS_SEQKIT" config './nextflow.config' tag "subworkflows" tag "subworkflows_nfcore" tag "subworkflows/fastq_sanitise_seqkit" - tag "subworkflows/fastq_preprocess" + tag "subworkflows/fastq_preprocess_seqkit" tag "seqkit" tag "seqkit/sana" tag "seqkit/pair" diff --git a/subworkflows/nf-core/fastq_preprocess/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_preprocess_seqkit/tests/main.nf.test.snap similarity index 59% rename from subworkflows/nf-core/fastq_preprocess/tests/main.nf.test.snap rename to subworkflows/nf-core/fastq_preprocess_seqkit/tests/main.nf.test.snap index 920809ca126f..84e40272fa44 100644 --- a/subworkflows/nf-core/fastq_preprocess/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_preprocess_seqkit/tests/main.nf.test.snap @@ -12,10 +12,10 @@ ] ], "1": [ - "versions.yml:md5,12eff6cdaef31b58e36df720f8d96331", - "versions.yml:md5,8352db48172cddc55e42f943cdee1b9a", - "versions.yml:md5,9afc673105901c4307e8bb20d367a3ce", - "versions.yml:md5,d4403f4032d4cbb377d61ed83712253e" + "versions.yml:md5,39b373e11c89d8445dd09c9ae185e543", + "versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd", + "versions.yml:md5,edb80840a6bf15376776a917a0f36216", + "versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6" ], "reads": [ [ @@ -27,30 +27,30 @@ ] ], "versions": [ - "versions.yml:md5,12eff6cdaef31b58e36df720f8d96331", - "versions.yml:md5,8352db48172cddc55e42f943cdee1b9a", - "versions.yml:md5,9afc673105901c4307e8bb20d367a3ce", - "versions.yml:md5,d4403f4032d4cbb377d61ed83712253e" + "versions.yml:md5,39b373e11c89d8445dd09c9ae185e543", + "versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd", + "versions.yml:md5,edb80840a6bf15376776a917a0f36216", + "versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6" ] }, [ { - "FASTQ_PREPROCESS:SEQKIT_REPLACE": { + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_REPLACE": { "seqkit": "2.9.0" } }, { - "FASTQ_PREPROCESS:SEQKIT_SEQ": { - "seqkit": "v2.9.0" + "FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": { + "seqkit": "2.10.1" } }, { - "FASTQ_PREPROCESS:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": { - "seqkit": "2.10.1" + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_RMDUP": { + "seqkit": "v2.9.0" } }, { - "FASTQ_PREPROCESS:SEQKIT_RMDUP": { + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_SEQ": { "seqkit": "v2.9.0" } } @@ -58,9 +58,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-10-29T13:17:10.915765" + "timestamp": "2025-12-09T16:30:14.034664087" }, "sarscov2 - fastq - single_end": { "content": [ @@ -75,10 +75,10 @@ ] ], "1": [ - "versions.yml:md5,12eff6cdaef31b58e36df720f8d96331", - "versions.yml:md5,8352db48172cddc55e42f943cdee1b9a", - "versions.yml:md5,9afc673105901c4307e8bb20d367a3ce", - "versions.yml:md5,d4403f4032d4cbb377d61ed83712253e" + "versions.yml:md5,39b373e11c89d8445dd09c9ae185e543", + "versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd", + "versions.yml:md5,edb80840a6bf15376776a917a0f36216", + "versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6" ], "reads": [ [ @@ -90,30 +90,30 @@ ] ], "versions": [ - "versions.yml:md5,12eff6cdaef31b58e36df720f8d96331", - "versions.yml:md5,8352db48172cddc55e42f943cdee1b9a", - "versions.yml:md5,9afc673105901c4307e8bb20d367a3ce", - "versions.yml:md5,d4403f4032d4cbb377d61ed83712253e" + "versions.yml:md5,39b373e11c89d8445dd09c9ae185e543", + "versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd", + "versions.yml:md5,edb80840a6bf15376776a917a0f36216", + "versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6" ] }, [ { - "FASTQ_PREPROCESS:SEQKIT_REPLACE": { + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_REPLACE": { "seqkit": "2.9.0" } }, { - "FASTQ_PREPROCESS:SEQKIT_SEQ": { - "seqkit": "v2.9.0" + "FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": { + "seqkit": "2.10.1" } }, { - "FASTQ_PREPROCESS:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": { - "seqkit": "2.10.1" + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_RMDUP": { + "seqkit": "v2.9.0" } }, { - "FASTQ_PREPROCESS:SEQKIT_RMDUP": { + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_SEQ": { "seqkit": "v2.9.0" } } @@ -121,9 +121,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-10-29T13:16:51.34468" + "timestamp": "2025-12-09T16:29:39.447454093" }, "sarscov2 - fastq - paired_end": { "content": [ @@ -141,10 +141,11 @@ ] ], "1": [ - "versions.yml:md5,12eff6cdaef31b58e36df720f8d96331", - "versions.yml:md5,8352db48172cddc55e42f943cdee1b9a", - "versions.yml:md5,9afc673105901c4307e8bb20d367a3ce", - "versions.yml:md5,d4403f4032d4cbb377d61ed83712253e" + "versions.yml:md5,29f612df1ac521c317aff0d7950e2ed6", + "versions.yml:md5,39b373e11c89d8445dd09c9ae185e543", + "versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd", + "versions.yml:md5,edb80840a6bf15376776a917a0f36216", + "versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6" ], "reads": [ [ @@ -159,30 +160,36 @@ ] ], "versions": [ - "versions.yml:md5,12eff6cdaef31b58e36df720f8d96331", - "versions.yml:md5,8352db48172cddc55e42f943cdee1b9a", - "versions.yml:md5,9afc673105901c4307e8bb20d367a3ce", - "versions.yml:md5,d4403f4032d4cbb377d61ed83712253e" + "versions.yml:md5,29f612df1ac521c317aff0d7950e2ed6", + "versions.yml:md5,39b373e11c89d8445dd09c9ae185e543", + "versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd", + "versions.yml:md5,edb80840a6bf15376776a917a0f36216", + "versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6" ] }, [ { - "FASTQ_PREPROCESS:SEQKIT_REPLACE": { + "FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_PAIR": { "seqkit": "2.9.0" } }, { - "FASTQ_PREPROCESS:SEQKIT_SEQ": { - "seqkit": "v2.9.0" + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_REPLACE": { + "seqkit": "2.9.0" } }, { - "FASTQ_PREPROCESS:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": { + "FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": { "seqkit": "2.10.1" } }, { - "FASTQ_PREPROCESS:SEQKIT_RMDUP": { + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_RMDUP": { + "seqkit": "v2.9.0" + } + }, + { + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_SEQ": { "seqkit": "v2.9.0" } } @@ -190,9 +197,9 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-10-29T13:16:58.073323" + "timestamp": "2025-12-09T16:29:51.089592083" }, "sarscov2 - fastq - both with single broken": { "content": [ @@ -217,10 +224,11 @@ ] ], "1": [ - "versions.yml:md5,12eff6cdaef31b58e36df720f8d96331", - "versions.yml:md5,8352db48172cddc55e42f943cdee1b9a", - "versions.yml:md5,9afc673105901c4307e8bb20d367a3ce", - "versions.yml:md5,d4403f4032d4cbb377d61ed83712253e" + "versions.yml:md5,29f612df1ac521c317aff0d7950e2ed6", + "versions.yml:md5,39b373e11c89d8445dd09c9ae185e543", + "versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd", + "versions.yml:md5,edb80840a6bf15376776a917a0f36216", + "versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6" ], "reads": [ [ @@ -242,30 +250,36 @@ ] ], "versions": [ - "versions.yml:md5,12eff6cdaef31b58e36df720f8d96331", - "versions.yml:md5,8352db48172cddc55e42f943cdee1b9a", - "versions.yml:md5,9afc673105901c4307e8bb20d367a3ce", - "versions.yml:md5,d4403f4032d4cbb377d61ed83712253e" + "versions.yml:md5,29f612df1ac521c317aff0d7950e2ed6", + "versions.yml:md5,39b373e11c89d8445dd09c9ae185e543", + "versions.yml:md5,adf5941e54371e92f795f80b8dc5abcd", + "versions.yml:md5,edb80840a6bf15376776a917a0f36216", + "versions.yml:md5,fe88ab8068d6a8284ee8a55f196f03e6" ] }, [ { - "FASTQ_PREPROCESS:SEQKIT_REPLACE": { + "FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_PAIR": { "seqkit": "2.9.0" } }, { - "FASTQ_PREPROCESS:SEQKIT_SEQ": { - "seqkit": "v2.9.0" + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_REPLACE": { + "seqkit": "2.9.0" } }, { - "FASTQ_PREPROCESS:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": { + "FASTQ_PREPROCESS_SEQKIT:FASTQ_SANITISE_SEQKIT:SEQKIT_SANA": { "seqkit": "2.10.1" } }, { - "FASTQ_PREPROCESS:SEQKIT_RMDUP": { + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_RMDUP": { + "seqkit": "v2.9.0" + } + }, + { + "FASTQ_PREPROCESS_SEQKIT:SEQKIT_SEQ": { "seqkit": "v2.9.0" } } @@ -273,8 +287,8 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.10.0" + "nextflow": "25.10.2" }, - "timestamp": "2025-10-29T13:17:05.485679" + "timestamp": "2025-12-09T16:30:03.379196661" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_preprocess/tests/nextflow.config b/subworkflows/nf-core/fastq_preprocess_seqkit/tests/nextflow.config similarity index 99% rename from subworkflows/nf-core/fastq_preprocess/tests/nextflow.config rename to subworkflows/nf-core/fastq_preprocess_seqkit/tests/nextflow.config index 97438b00ba0d..78045d7d3e04 100644 --- a/subworkflows/nf-core/fastq_preprocess/tests/nextflow.config +++ b/subworkflows/nf-core/fastq_preprocess_seqkit/tests/nextflow.config @@ -1,5 +1,4 @@ process { - withName: SEQKIT_SANA { ext.prefix = { "${meta.id}_${meta.strandness}" } } @@ -24,5 +23,4 @@ process { withName: SEQKIT_RMDUP { ext.prefix = { "${meta.id}_${meta.strandness}" } } - }