From 789613e502488eb65698af9e824ede11d4ecd5ee Mon Sep 17 00:00:00 2001 From: Charles Plessy Date: Wed, 19 Apr 2023 12:53:55 +0900 Subject: [PATCH 1/9] Update LAST to version 1453. --- modules/nf-core/last/dotplot/main.nf | 6 +++--- tests/modules/nf-core/last/dotplot/test.yml | 3 ++- 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/last/dotplot/main.nf b/modules/nf-core/last/dotplot/main.nf index a9c4462cfcd..2d91da352f1 100644 --- a/modules/nf-core/last/dotplot/main.nf +++ b/modules/nf-core/last/dotplot/main.nf @@ -2,10 +2,10 @@ process LAST_DOTPLOT { tag "$meta.id" label 'process_low' - conda "bioconda::last=1418" + conda "bioconda::last=1453" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1418--h5b5514e_0' : - 'quay.io/biocontainers/last:1418--h5b5514e_0' }" + 'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' : + 'quay.io/biocontainers/last:1453--h5b5514e_0' }" input: tuple val(meta), path(maf) diff --git a/tests/modules/nf-core/last/dotplot/test.yml b/tests/modules/nf-core/last/dotplot/test.yml index ceda8111257..03b0ecb1243 100644 --- a/tests/modules/nf-core/last/dotplot/test.yml +++ b/tests/modules/nf-core/last/dotplot/test.yml @@ -1,8 +1,9 @@ - name: last dotplot test_last_dotplot command: nextflow run ./tests/modules/nf-core/last/dotplot -entry test_last_dotplot -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/dotplot/nextflow.config tags: - - last/dotplot - last + - last/dotplot files: - path: output/last/test.png md5sum: 6189aaf96f522cdb664869724997bbcd + - path: output/last/versions.yml From 21126bf8f462d94492425340f7a434d0d7272f5b Mon Sep 17 00:00:00 2001 From: Charlotte Capitanchik Date: Wed, 19 Apr 2023 14:16:56 +0900 Subject: [PATCH 2/9] update lastdb version to 1453 --- modules/nf-core/last/lastdb/main.nf | 6 +++--- tests/modules/nf-core/last/lastdb/test.yml | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/last/lastdb/main.nf b/modules/nf-core/last/lastdb/main.nf index b7cbda01d83..a002fe13a8e 100644 --- a/modules/nf-core/last/lastdb/main.nf +++ b/modules/nf-core/last/lastdb/main.nf @@ -2,10 +2,10 @@ process LAST_LASTDB { tag "$meta.id" label 'process_medium' - conda "bioconda::last=1418" + conda "bioconda::last=1453" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1418--h5b5514e_0' : - 'quay.io/biocontainers/last:1418--h5b5514e_0' }" + 'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' : + 'quay.io/biocontainers/last:1453--h5b5514e_0' }" input: tuple val(meta), path(fastx) diff --git a/tests/modules/nf-core/last/lastdb/test.yml b/tests/modules/nf-core/last/lastdb/test.yml index 8001f49e554..7431c72c420 100644 --- a/tests/modules/nf-core/last/lastdb/test.yml +++ b/tests/modules/nf-core/last/lastdb/test.yml @@ -9,7 +9,7 @@ - path: output/last/lastdb/test.des md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc - path: output/last/lastdb/test.prj - md5sum: 0e570741b20e89e9878fe26f26d84b7a + md5sum: e90f43ca41802e0aa9e95348558c837e - path: output/last/lastdb/test.sds md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2 - path: output/last/lastdb/test.ssp @@ -23,15 +23,15 @@ - name: last lastdb test_last_lastdb_gzipped_input command: nextflow run ./tests/modules/nf-core/last/lastdb -entry test_last_lastdb_gzipped_input -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/lastdb/nextflow.config tags: - - last - last/lastdb + - last files: - path: output/last/lastdb/test.bck md5sum: 8692b1229b1fff1c2d39c4c610ff842b - path: output/last/lastdb/test.des md5sum: 26ab49015cc572172b9efa50fc5190bc - path: output/last/lastdb/test.prj - md5sum: b3e3b96d01ce4c2c5c88c85e4dc83453 + md5sum: dabf7db09dbae4c10af3246b56faeab7 - path: output/last/lastdb/test.sds md5sum: cad9927d4bd161257e98165ad755d8e4 - path: output/last/lastdb/test.ssp From 8b972ef9ee9673ac4bbdc6fd1daf1759ef77f919 Mon Sep 17 00:00:00 2001 From: Johannes Nicolaus Wibisana Date: Wed, 19 Apr 2023 14:32:40 +0900 Subject: [PATCH 3/9] update last mafconvert to 1453 --- modules/nf-core/last/mafconvert/main.nf | 6 +++--- tests/modules/nf-core/last/mafconvert/test.yml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/last/mafconvert/main.nf b/modules/nf-core/last/mafconvert/main.nf index 42e6b1aa1c1..1d9ac62ae59 100644 --- a/modules/nf-core/last/mafconvert/main.nf +++ b/modules/nf-core/last/mafconvert/main.nf @@ -2,10 +2,10 @@ process LAST_MAFCONVERT { tag "$meta.id" label 'process_high' - conda "bioconda::last=1418" + conda "bioconda::last=1453" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1418--h5b5514e_0' : - 'quay.io/biocontainers/last:1418--h5b5514e_0' }" + 'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' : + 'quay.io/biocontainers/last:1453--h5b5514e_0' }" input: tuple val(meta), path(maf) diff --git a/tests/modules/nf-core/last/mafconvert/test.yml b/tests/modules/nf-core/last/mafconvert/test.yml index 7daf124fc1f..98dc0ec468c 100644 --- a/tests/modules/nf-core/last/mafconvert/test.yml +++ b/tests/modules/nf-core/last/mafconvert/test.yml @@ -1,8 +1,8 @@ - name: last mafconvert test_last_mafconvert command: nextflow run ./tests/modules/nf-core/last/mafconvert -entry test_last_mafconvert -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/mafconvert/nextflow.config tags: - - last/mafconvert - last + - last/mafconvert files: - path: output/last/contigs.genome.psl.gz md5sum: 807889fbc4129884ae74c4ecf8804dde From ca545bf02da3570cec33ceac9b3ff3676b9edfb9 Mon Sep 17 00:00:00 2001 From: Johannes Nicolaus Wibisana Date: Wed, 19 Apr 2023 14:37:21 +0900 Subject: [PATCH 4/9] update last mafswap to 1453 --- modules/nf-core/last/mafswap/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/last/mafswap/main.nf b/modules/nf-core/last/mafswap/main.nf index 580a20d8b9b..cd1ddc7d351 100644 --- a/modules/nf-core/last/mafswap/main.nf +++ b/modules/nf-core/last/mafswap/main.nf @@ -2,10 +2,10 @@ process LAST_MAFSWAP { tag "$meta.id" label 'process_low' - conda "bioconda::last=1418" + conda "bioconda::last=1453" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1418--h5b5514e_0' : - 'quay.io/biocontainers/last:1418--h5b5514e_0' }" + 'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' : + 'quay.io/biocontainers/last:1453--h5b5514e_0' }" input: tuple val(meta), path(maf) From 6896e9eefda7d4a3d41b69c8f36f31b7c8e6d15d Mon Sep 17 00:00:00 2001 From: Charlotte Capitanchik Date: Wed, 19 Apr 2023 14:46:56 +0900 Subject: [PATCH 5/9] update postmask to last v1453 --- modules/nf-core/last/postmask/main.nf | 6 +++--- tests/modules/nf-core/last/postmask/test.yml | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/last/postmask/main.nf b/modules/nf-core/last/postmask/main.nf index eac417fbd76..0bcef7d4934 100644 --- a/modules/nf-core/last/postmask/main.nf +++ b/modules/nf-core/last/postmask/main.nf @@ -2,10 +2,10 @@ process LAST_POSTMASK { tag "$meta.id" label 'process_low' - conda "bioconda::last=1418" + conda "bioconda::last=1453" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1418--h5b5514e_0' : - 'quay.io/biocontainers/last:1418--h5b5514e_0' }" + 'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' : + 'quay.io/biocontainers/last:1453--h5b5514e_0' }" input: tuple val(meta), path(maf) diff --git a/tests/modules/nf-core/last/postmask/test.yml b/tests/modules/nf-core/last/postmask/test.yml index 0d3121d96ec..a84d91df887 100644 --- a/tests/modules/nf-core/last/postmask/test.yml +++ b/tests/modules/nf-core/last/postmask/test.yml @@ -1,8 +1,8 @@ - name: last postmask test_last_postmask command: nextflow run ./tests/modules/nf-core/last/postmask -entry test_last_postmask -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/last/postmask/nextflow.config tags: - - last - last/postmask + - last files: - path: output/last/contigs.genome.postmask.maf.gz md5sum: 3a0f42e76da9549748983ac4d7ff7473 From 3e1f64f91255fa053198248a48267186dbd74e01 Mon Sep 17 00:00:00 2001 From: Charlotte Capitanchik Date: Wed, 19 Apr 2023 14:48:23 +0900 Subject: [PATCH 6/9] update last split to v1453 --- modules/nf-core/last/split/main.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/last/split/main.nf b/modules/nf-core/last/split/main.nf index c42d02715be..b99b78e7167 100644 --- a/modules/nf-core/last/split/main.nf +++ b/modules/nf-core/last/split/main.nf @@ -2,10 +2,10 @@ process LAST_SPLIT { tag "$meta.id" label 'process_high' - conda "bioconda::last=1418" + conda "bioconda::last=1453" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1418--h5b5514e_0' : - 'quay.io/biocontainers/last:1418--h5b5514e_0' }" + 'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' : + 'quay.io/biocontainers/last:1453--h5b5514e_0' }" input: tuple val(meta), path(maf) From 7d8e565074eec3617c48048534541fae53abe483 Mon Sep 17 00:00:00 2001 From: Charlotte Capitanchik Date: Wed, 19 Apr 2023 14:50:27 +0900 Subject: [PATCH 7/9] last update train to v1453 --- modules/nf-core/last/train/main.nf | 6 +++--- tests/modules/nf-core/last/train/test.yml | 17 ++++++++++++++++- 2 files changed, 19 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/last/train/main.nf b/modules/nf-core/last/train/main.nf index 8905b59eb75..93ffac0c099 100644 --- a/modules/nf-core/last/train/main.nf +++ b/modules/nf-core/last/train/main.nf @@ -2,10 +2,10 @@ process LAST_TRAIN { tag "$meta.id" label 'process_high' - conda "bioconda::last=1418" + conda "bioconda::last=1453" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/last:1418--h5b5514e_0' : - 'quay.io/biocontainers/last:1418--h5b5514e_0' }" + 'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' : + 'quay.io/biocontainers/last:1453--h5b5514e_0' }" input: tuple val(meta), path(fastx) diff --git a/tests/modules/nf-core/last/train/test.yml b/tests/modules/nf-core/last/train/test.yml index d551a94d1be..b6015f0e6d1 100644 --- a/tests/modules/nf-core/last/train/test.yml +++ b/tests/modules/nf-core/last/train/test.yml @@ -5,5 +5,20 @@ - last files: - path: output/last/contigs.genome.par - md5sum: 457395281b6852cfee3417816e73a965 + md5sum: caf93e967179237a2eadbe4bae008c52 - path: output/last/versions.yml + - path: output/untar/lastdb/genome.bck + md5sum: 5519879b9b6c4d1fc508da7f17f88f2e + - path: output/untar/lastdb/genome.des + md5sum: 3a9ea6d336e113a74d7fdca5e7b623fc + - path: output/untar/lastdb/genome.prj + md5sum: 489715f14b0fea6273822696e72357f9 + - path: output/untar/lastdb/genome.sds + md5sum: 2cd381f4f8a9c52cfcd323a2863eccb2 + - path: output/untar/lastdb/genome.ssp + md5sum: 4137fb6fe9df2b3d78d5b960390aac7b + - path: output/untar/lastdb/genome.suf + md5sum: 1895efa8653e8e9bd3605cff0408ed33 + - path: output/untar/lastdb/genome.tis + md5sum: b7c40f06b1309dc6f37849eeb86dfd22 + - path: output/untar/versions.yml From 4b9e2168c7cd22c1d8a920c7a18755631c8a20ad Mon Sep 17 00:00:00 2001 From: Johannes Nicolaus Wibisana Date: Wed, 19 Jul 2023 15:37:17 +0900 Subject: [PATCH 8/9] Update meta.yml Change output value type to string --- modules/nf-core/last/mafconvert/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/last/mafconvert/meta.yml b/modules/nf-core/last/mafconvert/meta.yml index cd9633b70a7..daf85aca996 100644 --- a/modules/nf-core/last/mafconvert/meta.yml +++ b/modules/nf-core/last/mafconvert/meta.yml @@ -25,7 +25,7 @@ input: description: Multiple Aligment Format (MAF) file, optionally compressed with gzip pattern: "*.{maf.gz,maf}" - format: - type: value + type: string description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab) output: From d8f8d9718b5ec562ecfbc4687817fc499716c96a Mon Sep 17 00:00:00 2001 From: Johannes Nicolaus Wibisana Date: Wed, 19 Jul 2023 15:37:36 +0900 Subject: [PATCH 9/9] Update meta.yml Change output value type to string --- modules/nf-core/last/dotplot/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/last/dotplot/meta.yml b/modules/nf-core/last/dotplot/meta.yml index bddc2636f77..f6cfa016cbb 100644 --- a/modules/nf-core/last/dotplot/meta.yml +++ b/modules/nf-core/last/dotplot/meta.yml @@ -26,7 +26,7 @@ input: description: Multiple Aligment Format (MAF) file, compressed with gzip pattern: "*.{maf.gz}" - format: - type: value + type: string description: Output format (PNG or GIF). output: