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Update LAST modules to v1453 #3303

Merged
merged 18 commits into from
Jul 20, 2023
Merged

Update LAST modules to v1453 #3303

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789613e
Update LAST to version 1453.
charles-plessy Apr 19, 2023
21126bf
update lastdb version to 1453
CharlotteAnne Apr 19, 2023
8b972ef
update last mafconvert to 1453
johannesnicolaus Apr 19, 2023
ca545bf
update last mafswap to 1453
johannesnicolaus Apr 19, 2023
6896e9e
update postmask to last v1453
CharlotteAnne Apr 19, 2023
3e1f64f
update last split to v1453
CharlotteAnne Apr 19, 2023
7d8e565
last update train to v1453
CharlotteAnne Apr 19, 2023
6904e50
Merge pull request #1 from CharlotteAnne/update-lastdb
CharlotteAnne Apr 19, 2023
a682a7a
Merge pull request #2 from johannesnicolaus/dev_last_mafconvert
CharlotteAnne Apr 19, 2023
4426aa5
Merge pull request #3 from oist/update_last_doplot
CharlotteAnne Apr 19, 2023
594356d
Merge branch 'master' into update-last-modules
johannesnicolaus May 31, 2023
e10943c
Merge branch 'master' into update-last-modules
johannesnicolaus Jun 6, 2023
6c64ac4
Merge branch 'master' into update-last-modules
johannesnicolaus Jun 12, 2023
1bfc965
Merge branch 'master' into update-last-modules
johannesnicolaus Jul 12, 2023
ed38acd
Merge branch 'master' into update-last-modules
johannesnicolaus Jul 17, 2023
4b9e216
Update meta.yml
johannesnicolaus Jul 19, 2023
d8f8d97
Update meta.yml
johannesnicolaus Jul 19, 2023
8eb9ef9
Merge branch 'master' into update-last-modules
johannesnicolaus Jul 19, 2023
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6 changes: 3 additions & 3 deletions modules/nf-core/last/dotplot/main.nf
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Expand Up @@ -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' :
'biocontainers/last:1418--h5b5514e_0' }"
'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' :
'biocontainers/last:1453--h5b5514e_0' }"

input:
tuple val(meta), path(maf)
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2 changes: 1 addition & 1 deletion modules/nf-core/last/dotplot/meta.yml
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Expand Up @@ -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:
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6 changes: 3 additions & 3 deletions modules/nf-core/last/lastdb/main.nf
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Expand Up @@ -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' :
'biocontainers/last:1418--h5b5514e_0' }"
'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' :
'biocontainers/last:1453--h5b5514e_0' }"

input:
tuple val(meta), path(fastx)
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6 changes: 3 additions & 3 deletions modules/nf-core/last/mafconvert/main.nf
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Expand Up @@ -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' :
'biocontainers/last:1418--h5b5514e_0' }"
'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' :
'biocontainers/last:1453--h5b5514e_0' }"

input:
tuple val(meta), path(maf)
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2 changes: 1 addition & 1 deletion modules/nf-core/last/mafconvert/meta.yml
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Expand Up @@ -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:
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6 changes: 3 additions & 3 deletions modules/nf-core/last/mafswap/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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' :
'biocontainers/last:1418--h5b5514e_0' }"
'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' :
'biocontainers/last:1453--h5b5514e_0' }"

input:
tuple val(meta), path(maf)
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6 changes: 3 additions & 3 deletions modules/nf-core/last/postmask/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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' :
'biocontainers/last:1418--h5b5514e_0' }"
'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' :
'biocontainers/last:1453--h5b5514e_0' }"

input:
tuple val(meta), path(maf)
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6 changes: 3 additions & 3 deletions modules/nf-core/last/split/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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' :
'biocontainers/last:1418--h5b5514e_0' }"
'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' :
'biocontainers/last:1453--h5b5514e_0' }"

input:
tuple val(meta), path(maf)
Expand Down
6 changes: 3 additions & 3 deletions modules/nf-core/last/train/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -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' :
'biocontainers/last:1418--h5b5514e_0' }"
'https://depot.galaxyproject.org/singularity/last:1453--h5b5514e_0' :
'biocontainers/last:1453--h5b5514e_0' }"

input:
tuple val(meta), path(fastx)
Expand Down
3 changes: 2 additions & 1 deletion tests/modules/nf-core/last/dotplot/test.yml
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Original file line number Diff line number Diff line change
@@ -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
6 changes: 3 additions & 3 deletions tests/modules/nf-core/last/lastdb/test.yml
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Expand Up @@ -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
Expand All @@ -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
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2 changes: 1 addition & 1 deletion tests/modules/nf-core/last/mafconvert/test.yml
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Original file line number Diff line number Diff line change
@@ -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
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2 changes: 1 addition & 1 deletion tests/modules/nf-core/last/postmask/test.yml
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@@ -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
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17 changes: 16 additions & 1 deletion tests/modules/nf-core/last/train/test.yml
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Expand Up @@ -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
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