Update LAST modules to v1453 (nf-core#3303)

* Update LAST to version 1453. * update lastdb version to 1453 * update last mafconvert to 1453 * update last mafswap to 1453 * update postmask to last v1453 * update last split to v1453 * last update train to v1453 * Update meta.yml Change output value type to string * Update meta.yml Change output value type to string --------- Co-authored-by: Charles Plessy <charles.plessy@oist.jp> Co-authored-by: Charlotte Capitanchik <charlotte.capitanchik@crick.ac.uk> Co-authored-by: Johannes Nicolaus Wibisana <johannes.nicolaus@oist.jp> Co-authored-by: Charlotte Capitanchik <CharlotteAnne@users.noreply.github.com>
limrp · Jul 28, 2023 · 5f017ea · 5f017ea
1 parent 9134e17
commit 5f017ea
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Showing 14 changed files with 46 additions and 30 deletions.
diff --git 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' :
-        '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)

diff --git 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:

diff --git 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' :
-        '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)

diff --git 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' :
-        '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)

diff --git 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:

diff --git 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' :
-        '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)

diff --git 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' :
-        '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)

diff --git 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' :
-        '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)

diff --git 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' :
-        '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)

diff --git 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
diff --git 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

diff --git 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

diff --git 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

diff --git 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