From 550390345785fe0ebb1835616f895af2bdadf122 Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Tue, 3 May 2022 09:46:04 +0200 Subject: [PATCH 1/6] Add compression for output fastq file --- modules/samtools/bam2fq/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf index 5d6aa79d..554af48b 100644 --- a/modules/samtools/bam2fq/main.nf +++ b/modules/samtools/bam2fq/main.nf @@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ { bam2fq \\ $args \\ -@ $task.cpus \\ - $inputbam >${prefix}_interleaved.fq.gz + $inputbam | gzip > ${prefix}_interleaved.fq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": From 59d6e6e1dd0dc5cbfff7d431725caeaf201c40e4 Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Tue, 3 May 2022 09:56:50 +0200 Subject: [PATCH 2/6] Add updated md5sums --- tests/modules/samtools/bam2fq/test.yml | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml index 213c7a2d..6fcc9c22 100644 --- a/tests/modules/samtools/bam2fq/test.yml +++ b/tests/modules/samtools/bam2fq/test.yml @@ -1,17 +1,19 @@ - name: samtools bam2fq test_samtools_bam2fq_nosplit - command: nextflow run ./tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bam2fq/nextflow.config + command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c tests/config/nextflow.config tags: - - samtools/bam2fq - samtools + - samtools/bam2fq files: - path: output/samtools/test_interleaved.fq.gz - md5sum: d733e66d29a4b366bf9df8c42f845256 + md5sum: 7a57a8ab53dd1d799cca67a85c47ccd9 + - path: output/samtools/versions.yml + md5sum: 4973eac1b6a8f090d5fcd4456d65a894 - name: samtools bam2fq test_samtools_bam2fq_withsplit - command: nextflow run ./tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c ./tests/config/nextflow.config -c ./tests/modules/samtools/bam2fq/nextflow.config + command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c tests/config/nextflow.config tags: - - samtools/bam2fq - samtools + - samtools/bam2fq files: - path: output/samtools/test_1.fq.gz md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed @@ -21,3 +23,5 @@ md5sum: 709872fc2910431b1e8b7074bfe38c67 - path: output/samtools/test_singleton.fq.gz md5sum: 709872fc2910431b1e8b7074bfe38c67 + - path: output/samtools/versions.yml + md5sum: e92d21bbcda2fed7cb438d95c51edff0 From 5510ea39fe638594bc26ac34cadf4a84bf27d159 Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Tue, 3 May 2022 15:18:09 +0200 Subject: [PATCH 3/6] Test --no-name to solve inconsistent checksums --- modules/samtools/bam2fq/main.nf | 2 +- tests/modules/samtools/bam2fq/test.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/samtools/bam2fq/main.nf b/modules/samtools/bam2fq/main.nf index 554af48b..9301d1d3 100644 --- a/modules/samtools/bam2fq/main.nf +++ b/modules/samtools/bam2fq/main.nf @@ -45,7 +45,7 @@ process SAMTOOLS_BAM2FQ { bam2fq \\ $args \\ -@ $task.cpus \\ - $inputbam | gzip > ${prefix}_interleaved.fq.gz + $inputbam | gzip --no-name > ${prefix}_interleaved.fq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml index 6fcc9c22..674730d7 100644 --- a/tests/modules/samtools/bam2fq/test.yml +++ b/tests/modules/samtools/bam2fq/test.yml @@ -1,8 +1,8 @@ - name: samtools bam2fq test_samtools_bam2fq_nosplit command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_nosplit -c tests/config/nextflow.config tags: - - samtools - samtools/bam2fq + - samtools files: - path: output/samtools/test_interleaved.fq.gz md5sum: 7a57a8ab53dd1d799cca67a85c47ccd9 @@ -12,8 +12,8 @@ - name: samtools bam2fq test_samtools_bam2fq_withsplit command: nextflow run tests/modules/samtools/bam2fq -entry test_samtools_bam2fq_withsplit -c tests/config/nextflow.config tags: - - samtools - samtools/bam2fq + - samtools files: - path: output/samtools/test_1.fq.gz md5sum: 1c84aadcdca10e97be2b5b6ce773f5ed From a39fa4e003efce395debe34de57c5b28472c762c Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Tue, 3 May 2022 15:47:49 +0200 Subject: [PATCH 4/6] Fix checksum for one file --- tests/modules/samtools/bam2fq/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml index 674730d7..9d641e4a 100644 --- a/tests/modules/samtools/bam2fq/test.yml +++ b/tests/modules/samtools/bam2fq/test.yml @@ -5,7 +5,7 @@ - samtools files: - path: output/samtools/test_interleaved.fq.gz - md5sum: 7a57a8ab53dd1d799cca67a85c47ccd9 + md5sum: 7290d2d8dbef0fa57c0e2f28b5db1bf8 - path: output/samtools/versions.yml md5sum: 4973eac1b6a8f090d5fcd4456d65a894 From be8ce6de2ae833802a44b9c2b3991dbb56eb43a4 Mon Sep 17 00:00:00 2001 From: ljmesi <37740329+ljmesi@users.noreply.github.com> Date: Thu, 5 May 2022 08:32:45 +0200 Subject: [PATCH 5/6] Remove variable md5sum from the tests --- tests/modules/samtools/bam2fq/test.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/tests/modules/samtools/bam2fq/test.yml b/tests/modules/samtools/bam2fq/test.yml index 9d641e4a..4f9472e5 100644 --- a/tests/modules/samtools/bam2fq/test.yml +++ b/tests/modules/samtools/bam2fq/test.yml @@ -5,7 +5,6 @@ - samtools files: - path: output/samtools/test_interleaved.fq.gz - md5sum: 7290d2d8dbef0fa57c0e2f28b5db1bf8 - path: output/samtools/versions.yml md5sum: 4973eac1b6a8f090d5fcd4456d65a894 From 40dd662fd26c3eb3160b7c8cbbe9bff80bbe2c30 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Thu, 5 May 2022 12:57:14 +0200 Subject: [PATCH 6/6] update ensemblvep and snpeff modules --- modules/ensemblvep/Dockerfile | 11 +++-- modules/ensemblvep/build.sh | 5 +- modules/ensemblvep/main.nf | 1 + modules/ensemblvep/meta.yml | 15 ++---- modules/snpeff/Dockerfile | 9 ++-- modules/snpeff/build.sh | 5 +- modules/snpeff/meta.yml | 12 ----- .../nf-core/annotation/ensemblvep/main.nf | 31 ++++++++++++ .../nf-core/annotation/ensemblvep/meta.yml | 49 +++++++++++++++++++ .../nf-core/annotation/snpeff/main.nf | 28 +++++++++++ .../snpeff}/meta.yml | 18 +++++-- .../nf-core/annotation_ensemblvep/main.nf | 26 ---------- .../nf-core/annotation_ensemblvep/meta.yml | 29 ----------- .../nf-core/annotation_snpeff/main.nf | 23 --------- tests/modules/ensemblvep/main.nf | 2 +- .../ensemblvep}/main.nf | 4 +- .../ensemblvep}/nextflow.config | 2 +- .../ensemblvep}/test.yml | 0 .../snpeff}/main.nf | 2 +- .../snpeff}/nextflow.config | 2 +- .../snpeff}/test.yml | 0 21 files changed, 149 insertions(+), 125 deletions(-) mode change 100755 => 100644 modules/snpeff/build.sh create mode 100644 subworkflows/nf-core/annotation/ensemblvep/main.nf create mode 100644 subworkflows/nf-core/annotation/ensemblvep/meta.yml create mode 100644 subworkflows/nf-core/annotation/snpeff/main.nf rename subworkflows/nf-core/{annotation_snpeff => annotation/snpeff}/meta.yml (66%) delete mode 100644 subworkflows/nf-core/annotation_ensemblvep/main.nf delete mode 100644 subworkflows/nf-core/annotation_ensemblvep/meta.yml delete mode 100644 subworkflows/nf-core/annotation_snpeff/main.nf rename tests/subworkflows/nf-core/{annotation_ensemblvep => annotation/ensemblvep}/main.nf (69%) rename tests/subworkflows/nf-core/{annotation_ensemblvep => annotation/ensemblvep}/nextflow.config (88%) rename tests/subworkflows/nf-core/{annotation_ensemblvep => annotation/ensemblvep}/test.yml (100%) rename tests/subworkflows/nf-core/{annotation_snpeff => annotation/snpeff}/main.nf (74%) rename tests/subworkflows/nf-core/{annotation_snpeff => annotation/snpeff}/nextflow.config (88%) rename tests/subworkflows/nf-core/{annotation_snpeff => annotation/snpeff}/test.yml (100%) diff --git a/modules/ensemblvep/Dockerfile b/modules/ensemblvep/Dockerfile index ac1b4691..b4a1c664 100644 --- a/modules/ensemblvep/Dockerfile +++ b/modules/ensemblvep/Dockerfile @@ -8,13 +8,14 @@ LABEL \ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -# Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-vep-104.3/bin:$PATH - # Setup default ARG variables ARG GENOME=GRCh38 ARG SPECIES=homo_sapiens -ARG VEP_VERSION=99 +ARG VEP_VERSION=104 +ARG VEP_TAG=104.3 + +# Add conda installation dir to PATH (instead of doing 'conda activate') +ENV PATH /opt/conda/envs/nf-core-vep-${VEP_TAG}/bin:$PATH # Download Genome RUN vep_install \ @@ -27,4 +28,4 @@ RUN vep_install \ --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-vep-104.3 > nf-core-vep-104.3.yml +RUN conda env export --name nf-core-vep-${VEP_TAG} > nf-core-vep-${VEP_TAG}.yml diff --git a/modules/ensemblvep/build.sh b/modules/ensemblvep/build.sh index 5fcb91df..650c8704 100755 --- a/modules/ensemblvep/build.sh +++ b/modules/ensemblvep/build.sh @@ -10,11 +10,12 @@ build_push() { VEP_TAG=$4 docker build \ + . \ -t nfcore/vep:${VEP_TAG}.${GENOME} \ - software/vep/. \ --build-arg GENOME=${GENOME} \ --build-arg SPECIES=${SPECIES} \ - --build-arg VEP_VERSION=${VEP_VERSION} + --build-arg VEP_VERSION=${VEP_VERSION} \ + --build-arg VEP_TAG=${VEP_TAG} docker push nfcore/vep:${VEP_TAG}.${GENOME} } diff --git a/modules/ensemblvep/main.nf b/modules/ensemblvep/main.nf index c2bd055f..a5a9b1ab 100644 --- a/modules/ensemblvep/main.nf +++ b/modules/ensemblvep/main.nf @@ -13,6 +13,7 @@ process ENSEMBLVEP { val species val cache_version path cache + path extra_files output: tuple val(meta), path("*.ann.vcf"), emit: vcf diff --git a/modules/ensemblvep/meta.yml b/modules/ensemblvep/meta.yml index cd9c8905..418bb970 100644 --- a/modules/ensemblvep/meta.yml +++ b/modules/ensemblvep/meta.yml @@ -10,17 +10,6 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] -params: - - use_cache: - type: boolean - description: | - Enable the usage of containers with cache - Does not work with conda - - vep_tag: - type: value - description: | - Specify the tag for the container - https://hub.docker.com/r/nfcore/vep/tags input: - meta: type: map @@ -47,6 +36,10 @@ input: type: file description: | path to VEP cache (optional) + - extra_files: + type: tuple + description: | + path to file(s) needed for plugins (optional) output: - vcf: type: file diff --git a/modules/snpeff/Dockerfile b/modules/snpeff/Dockerfile index 608716a4..d0e34757 100644 --- a/modules/snpeff/Dockerfile +++ b/modules/snpeff/Dockerfile @@ -8,15 +8,16 @@ LABEL \ COPY environment.yml / RUN conda env create -f /environment.yml && conda clean -a -# Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-snpeff-5.0/bin:$PATH - # Setup default ARG variables ARG GENOME=GRCh38 ARG SNPEFF_CACHE_VERSION=99 +ARG SNPEFF_TAG=99 + +# Add conda installation dir to PATH (instead of doing 'conda activate') +ENV PATH /opt/conda/envs/nf-core-snpeff-${SNPEFF_TAG}/bin:$PATH # Download Genome RUN snpEff download -v ${GENOME}.${SNPEFF_CACHE_VERSION} # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-snpeff-5.0 > nf-core-snpeff-5.0.yml +RUN conda env export --name nf-core-snpeff-${SNPEFF_TAG} > nf-core-snpeff-${SNPEFF_TAG}.yml diff --git a/modules/snpeff/build.sh b/modules/snpeff/build.sh old mode 100755 new mode 100644 index b94ffd69..2fccf9a8 --- a/modules/snpeff/build.sh +++ b/modules/snpeff/build.sh @@ -9,10 +9,11 @@ build_push() { SNPEFF_TAG=$3 docker build \ + . \ -t nfcore/snpeff:${SNPEFF_TAG}.${GENOME} \ - software/snpeff/. \ --build-arg GENOME=${GENOME} \ - --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION} + --build-arg SNPEFF_CACHE_VERSION=${SNPEFF_CACHE_VERSION} \ + --build-arg SNPEFF_TAG=${SNPEFF_TAG} docker push nfcore/snpeff:${SNPEFF_TAG}.${GENOME} } diff --git a/modules/snpeff/meta.yml b/modules/snpeff/meta.yml index c191b9ac..2f0d866e 100644 --- a/modules/snpeff/meta.yml +++ b/modules/snpeff/meta.yml @@ -10,18 +10,6 @@ tools: homepage: https://pcingola.github.io/SnpEff/ documentation: https://pcingola.github.io/SnpEff/se_introduction/ licence: ["MIT"] -params: - - use_cache: - type: boolean - description: | - boolean to enable the usage of containers with cache - Enable the usage of containers with cache - Does not work with conda - - snpeff_tag: - type: value - description: | - Specify the tag for the container - https://hub.docker.com/r/nfcore/snpeff/tags input: - meta: type: map diff --git a/subworkflows/nf-core/annotation/ensemblvep/main.nf b/subworkflows/nf-core/annotation/ensemblvep/main.nf new file mode 100644 index 00000000..5073f38d --- /dev/null +++ b/subworkflows/nf-core/annotation/ensemblvep/main.nf @@ -0,0 +1,31 @@ +// +// Run VEP to annotate VCF files +// + +include { ENSEMBLVEP } from '../../../../modules/ensemblvep/main' +include { TABIX_BGZIPTABIX } from '../../../../modules/tabix/bgziptabix/main' + +workflow ANNOTATION_ENSEMBLVEP { + take: + vcf // channel: [ val(meta), vcf ] + vep_genome // value: genome to use + vep_species // value: species to use + vep_cache_version // value: cache version to use + vep_cache // path: /path/to/vep/cache (optionnal) + vep_extra_files // channel: [ file1, file2...] (optionnal) + + main: + ch_versions = Channel.empty() + + ENSEMBLVEP(vcf, vep_genome, vep_species, vep_cache_version, vep_cache, vep_extra_files) + TABIX_BGZIPTABIX(ENSEMBLVEP.out.vcf) + + // Gather versions of all tools used + ch_versions = ch_versions.mix(ENSEMBLVEP.out.versions.first()) + ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions.first()) + + emit: + vcf_tbi = TABIX_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] + reports = ENSEMBLVEP.out.report // path: *.html + versions = ch_versions // path: versions.yml +} diff --git a/subworkflows/nf-core/annotation/ensemblvep/meta.yml b/subworkflows/nf-core/annotation/ensemblvep/meta.yml new file mode 100644 index 00000000..585e003b --- /dev/null +++ b/subworkflows/nf-core/annotation/ensemblvep/meta.yml @@ -0,0 +1,49 @@ +name: annotation_ensemblvep +description: | + Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file +keywords: + - ensemblvep +modules: + - ensemblvep + - tabix/bgziptabix +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + - genome: + type: value + description: | + which genome to annotate with + - species: + type: value + description: | + which species to annotate with + - cache_version: + type: value + description: | + which version of the cache to annotate with + - cache: + type: file + description: | + path to VEP cache (optional) + - extra_files: + type: tuple + description: | + path to file(s) needed for plugins (optional) +output: + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - vcf_tbi: + type: file + description: Compressed vcf file + tabix index + pattern: "[ *{.vcf.gz,vcf.gz.tbi} ]" +authors: + - "@maxulysse" diff --git a/subworkflows/nf-core/annotation/snpeff/main.nf b/subworkflows/nf-core/annotation/snpeff/main.nf new file mode 100644 index 00000000..dcf06eb0 --- /dev/null +++ b/subworkflows/nf-core/annotation/snpeff/main.nf @@ -0,0 +1,28 @@ +// +// Run SNPEFF to annotate VCF files +// + +include { SNPEFF } from '../../../../modules/snpeff/main' +include { TABIX_BGZIPTABIX } from '../../../../modules/tabix/bgziptabix/main' + +workflow ANNOTATION_SNPEFF { + take: + vcf // channel: [ val(meta), vcf ] + snpeff_db // value: db version to use + snpeff_cache // path: /path/to/snpeff/cache (optionnal) + + main: + ch_versions = Channel.empty() + + SNPEFF(vcf, snpeff_db, snpeff_cache) + TABIX_BGZIPTABIX(SNPEFF.out.vcf) + + // Gather versions of all tools used + ch_versions = ch_versions.mix(SNPEFF.out.versions.first()) + ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions.first()) + + emit: + vcf_tbi = TABIX_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] + reports = SNPEFF.out.report // path: *.html + versions = ch_versions // path: versions.yml +} diff --git a/subworkflows/nf-core/annotation_snpeff/meta.yml b/subworkflows/nf-core/annotation/snpeff/meta.yml similarity index 66% rename from subworkflows/nf-core/annotation_snpeff/meta.yml rename to subworkflows/nf-core/annotation/snpeff/meta.yml index e0773626..241a00cc 100644 --- a/subworkflows/nf-core/annotation_snpeff/meta.yml +++ b/subworkflows/nf-core/annotation/snpeff/meta.yml @@ -11,11 +11,19 @@ input: type: map description: | Groovy Map containing sample information - e.g. [ id:'test' ] - - input: - type: vcf - description: list containing one vcf file - pattern: "[ *.{vcf,vcf.gz} ]" + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + - db: + type: value + description: | + which db to annotate with + - cache: + type: file + description: | + path to snpEff cache (optional) output: - versions: type: file diff --git a/subworkflows/nf-core/annotation_ensemblvep/main.nf b/subworkflows/nf-core/annotation_ensemblvep/main.nf deleted file mode 100644 index 3f3ecc6e..00000000 --- a/subworkflows/nf-core/annotation_ensemblvep/main.nf +++ /dev/null @@ -1,26 +0,0 @@ -// -// Run VEP to annotate VCF files -// - -include { ENSEMBLVEP } from '../../../modules/ensemblvep/main' -include { TABIX_BGZIPTABIX as ANNOTATION_BGZIPTABIX } from '../../../modules/tabix/bgziptabix/main' - -workflow ANNOTATION_ENSEMBLVEP { - take: - vcf // channel: [ val(meta), vcf ] - vep_genome // value: which genome - vep_species // value: which species - vep_cache_version // value: which cache version - vep_cache // path: path_to_vep_cache (optionnal) - - main: - ENSEMBLVEP(vcf, vep_genome, vep_species, vep_cache_version, vep_cache) - ANNOTATION_BGZIPTABIX(ENSEMBLVEP.out.vcf) - - ch_versions = ENSEMBLVEP.out.versions.first().mix(ANNOTATION_BGZIPTABIX.out.versions.first()) - - emit: - vcf_tbi = ANNOTATION_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] - reports = ENSEMBLVEP.out.report // path: *.html - versions = ch_versions // path: versions.yml -} diff --git a/subworkflows/nf-core/annotation_ensemblvep/meta.yml b/subworkflows/nf-core/annotation_ensemblvep/meta.yml deleted file mode 100644 index 991a8b2f..00000000 --- a/subworkflows/nf-core/annotation_ensemblvep/meta.yml +++ /dev/null @@ -1,29 +0,0 @@ -name: annotation_ensemblvep -description: | - Perform annotation with ensemblvep and bgzip + tabix index the resulting VCF file -keywords: - - ensemblvep -modules: - - ensemblvep - - tabix/bgziptabix -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input: - type: vcf - description: list containing one vcf file - pattern: "[ *.{vcf,vcf.gz} ]" -output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - vcf_tbi: - type: file - description: Compressed vcf file + tabix index - pattern: "[ *{.vcf.gz,vcf.gz.tbi} ]" -authors: - - "@maxulysse" diff --git a/subworkflows/nf-core/annotation_snpeff/main.nf b/subworkflows/nf-core/annotation_snpeff/main.nf deleted file mode 100644 index add5f9c8..00000000 --- a/subworkflows/nf-core/annotation_snpeff/main.nf +++ /dev/null @@ -1,23 +0,0 @@ -// -// Run SNPEFF to annotate VCF files -// - -include { SNPEFF } from '../../../modules/snpeff/main' -include { TABIX_BGZIPTABIX as ANNOTATION_BGZIPTABIX } from '../../../modules/tabix/bgziptabix/main' - -workflow ANNOTATION_SNPEFF { - take: - vcf // channel: [ val(meta), vcf ] - snpeff_db // value: version of db to use - snpeff_cache // path: path_to_snpeff_cache (optionnal) - - main: - SNPEFF(vcf, snpeff_db, snpeff_cache) - ANNOTATION_BGZIPTABIX(SNPEFF.out.vcf) - ch_versions = SNPEFF.out.versions.first().mix(ANNOTATION_BGZIPTABIX.out.versions.first()) - - emit: - vcf_tbi = ANNOTATION_BGZIPTABIX.out.gz_tbi // channel: [ val(meta), vcf.gz, vcf.gz.tbi ] - reports = SNPEFF.out.report // path: *.html - versions = ch_versions // path: versions.yml -} diff --git a/tests/modules/ensemblvep/main.nf b/tests/modules/ensemblvep/main.nf index 223847c7..30d19957 100644 --- a/tests/modules/ensemblvep/main.nf +++ b/tests/modules/ensemblvep/main.nf @@ -10,5 +10,5 @@ workflow test_ensemblvep { file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ] - ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [] ) + ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [] ) } diff --git a/tests/subworkflows/nf-core/annotation_ensemblvep/main.nf b/tests/subworkflows/nf-core/annotation/ensemblvep/main.nf similarity index 69% rename from tests/subworkflows/nf-core/annotation_ensemblvep/main.nf rename to tests/subworkflows/nf-core/annotation/ensemblvep/main.nf index 0f00c62e..2c599671 100644 --- a/tests/subworkflows/nf-core/annotation_ensemblvep/main.nf +++ b/tests/subworkflows/nf-core/annotation/ensemblvep/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ANNOTATION_ENSEMBLVEP } from '../../../../subworkflows/nf-core/annotation_ensemblvep/main' +include { ANNOTATION_ENSEMBLVEP } from '../../../../../subworkflows/nf-core/annotation/ensemblvep/main' workflow annotation_ensemblvep { input = [ @@ -10,5 +10,5 @@ workflow annotation_ensemblvep { file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ] - ANNOTATION_ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [] ) + ANNOTATION_ENSEMBLVEP ( input, "WBcel235", "caenorhabditis_elegans", "104", [], [] ) } diff --git a/tests/subworkflows/nf-core/annotation_ensemblvep/nextflow.config b/tests/subworkflows/nf-core/annotation/ensemblvep/nextflow.config similarity index 88% rename from tests/subworkflows/nf-core/annotation_ensemblvep/nextflow.config rename to tests/subworkflows/nf-core/annotation/ensemblvep/nextflow.config index 4e8d2990..806adb58 100644 --- a/tests/subworkflows/nf-core/annotation_ensemblvep/nextflow.config +++ b/tests/subworkflows/nf-core/annotation/ensemblvep/nextflow.config @@ -7,7 +7,7 @@ process { publishDir = [ enabled: false ] } - withName: ANNOTATION_BGZIPTABIX { + withName: TABIX_BGZIPTABIX { ext.prefix = { "${meta.id}_VEP.ann.vcf" } } diff --git a/tests/subworkflows/nf-core/annotation_ensemblvep/test.yml b/tests/subworkflows/nf-core/annotation/ensemblvep/test.yml similarity index 100% rename from tests/subworkflows/nf-core/annotation_ensemblvep/test.yml rename to tests/subworkflows/nf-core/annotation/ensemblvep/test.yml diff --git a/tests/subworkflows/nf-core/annotation_snpeff/main.nf b/tests/subworkflows/nf-core/annotation/snpeff/main.nf similarity index 74% rename from tests/subworkflows/nf-core/annotation_snpeff/main.nf rename to tests/subworkflows/nf-core/annotation/snpeff/main.nf index c80197ee..4aee20ee 100644 --- a/tests/subworkflows/nf-core/annotation_snpeff/main.nf +++ b/tests/subworkflows/nf-core/annotation/snpeff/main.nf @@ -2,7 +2,7 @@ nextflow.enable.dsl = 2 -include { ANNOTATION_SNPEFF } from '../../../../subworkflows/nf-core/annotation_snpeff/main' +include { ANNOTATION_SNPEFF } from '../../../../../subworkflows/nf-core/annotation_snpeff/main' workflow annotation_snpeff { input = [ diff --git a/tests/subworkflows/nf-core/annotation_snpeff/nextflow.config b/tests/subworkflows/nf-core/annotation/snpeff/nextflow.config similarity index 88% rename from tests/subworkflows/nf-core/annotation_snpeff/nextflow.config rename to tests/subworkflows/nf-core/annotation/snpeff/nextflow.config index be76cb4a..31fd635b 100644 --- a/tests/subworkflows/nf-core/annotation_snpeff/nextflow.config +++ b/tests/subworkflows/nf-core/annotation/snpeff/nextflow.config @@ -7,7 +7,7 @@ process { publishDir = [ enabled: false ] } - withName: ANNOTATION_BGZIPTABIX { + withName: TABIX_BGZIPTABIX { ext.prefix = { "${meta.id}_snpEff.ann.vcf" } } diff --git a/tests/subworkflows/nf-core/annotation_snpeff/test.yml b/tests/subworkflows/nf-core/annotation/snpeff/test.yml similarity index 100% rename from tests/subworkflows/nf-core/annotation_snpeff/test.yml rename to tests/subworkflows/nf-core/annotation/snpeff/test.yml