Bump star version and port tests to nf-test

modules/nf-core/star/align/environment.yml

@@ -4,7 +4,5 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::star=2.7.10a
-  - bioconda::samtools=1.18
-  - bioconda::htslib=1.18
-  - conda-forge::gawk=5.1.0
+  - bioconda::htslib=1.19.1
+  - bioconda::star=2.7.11b

modules/nf-core/star/align/main.nf

@@ -4,8 +4,8 @@ process STAR_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' :
-        'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:ded3841da0194af2701c780e9b3d653a85d27489-0' }"
+        'https://depot.galaxyproject.org/singularity/star:2.7.11b--h43eeafb_1' :
+        'biocontainers/star:2.7.11b--h43eeafb_1' }"
 
     input:
     tuple val(meta), path(reads, stageAs: "input*/*")
@@ -73,8 +73,6 @@ process STAR_ALIGN {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         star: \$(STAR --version | sed -e "s/STAR_//g")
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
     END_VERSIONS
     """
 
@@ -102,8 +100,6 @@ process STAR_ALIGN {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         star: \$(STAR --version | sed -e "s/STAR_//g")
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-        gawk: \$(echo \$(gawk --version 2>&1) | sed 's/^.*GNU Awk //; s/, .*\$//')
     END_VERSIONS
     """
 }

modules/nf-core/star/align/tests/main.nf.test

@@ -19,6 +19,10 @@ nextflow_process {
                     [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
                 ])
                 input[1] = Channel.of([
+                    [ id:'test_fai' ],
+                    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ]
+                ])
+                input[2] = Channel.of([
                     [ id:'test_gtf' ],
                     [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ]
                 ])