Version bumps and minor module updates (#406)

* Version bumps and minor module updates

* Fix Pangolin tests

* Fix SPAdes tests

* stageAs @phue

software/pangolin/main.nf

@@ -11,11 +11,11 @@ process PANGOLIN {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? 'bioconda::pangolin=2.3.2' : null)
+    conda (params.enable_conda ? 'bioconda::pangolin=2.3.8' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.2--py_0'
+        container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.8--py_0'
     } else {
-        container 'quay.io/biocontainers/pangolin:2.3.2--py_0'
+        container 'quay.io/biocontainers/pangolin:2.3.8--py_0'
     }
 
     input:

software/rsem/preparereference/main.nf

@@ -19,12 +19,13 @@ process RSEM_PREPAREREFERENCE {
     }
 
     input:
-    path fasta
+    path fasta, stageAs: "rsem/*"
     path gtf
 
     output:
-    path "rsem"         , emit: index
+    path "rsem"                , emit: index
-    path "*.version.txt", emit: version
+    path "rsem/*transcripts.fa", emit: transcript_fasta
+    path "*.version.txt"       , emit: version
 
     script:
     def software = getSoftwareName(task.process)
@@ -33,7 +34,6 @@ process RSEM_PREPAREREFERENCE {
         args.removeIf { it.contains('--star') }
         def memory = task.memory ? "--limitGenomeGenerateRAM ${task.memory.toBytes() - 100000000}" : ''
         """
-        mkdir rsem
         STAR \\
             --runMode genomeGenerate \\
             --genomeDir rsem/ \\
@@ -54,7 +54,6 @@ process RSEM_PREPAREREFERENCE {
         """
     } else {
         """
-        mkdir rsem
         rsem-prepare-reference \\
             --gtf $gtf \\
             --num-threads $task.cpus \\

software/spades/main.nf

@@ -11,17 +11,16 @@ process SPADES {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? "bioconda::spades=3.15.0" : null)
+    conda (params.enable_conda ? "bioconda::spades=3.15.2" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/spades:3.15.0--h633aebb_0"
+        container "https://depot.galaxyproject.org/singularity/spades:3.15.2--h95f258a_1"
     } else {
-        container "quay.io/biocontainers/spades:3.15.0--h633aebb_0"
+        container "quay.io/biocontainers/spades:3.15.2--h95f258a_1"
     }
 
     input:
     tuple val(meta), path(reads)
     path  hmm
-    val   coronaspades
 
     output:
     tuple val(meta), path('*.scaffolds.fa')    , optional:true, emit: scaffolds
@@ -37,9 +36,8 @@ process SPADES {
     def prefix      = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     def input_reads = meta.single_end ? "-s $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
     def custom_hmms = params.spades_hmm ? "--custom-hmms $hmm" : ""
-    def command     = coronaspades ? "coronaspades.py" : "spades.py"
     """
-    $command \\
+    spades.py \\
         $options.args \\
         --threads $task.cpus \\
         $custom_hmms \\

software/spades/meta.yml

@@ -29,11 +29,6 @@ input:
       type: file
       description:
         File or directory with amino acid HMMs for Spades HMM-guided mode.
-  - coronaspades:
-      type: boolean
-      description: |
-        Run coronaspades instead of default spades mode. coronaSPAdes is a special
-        mode of rnaviralSPAdes specifically aimed for SARS-CoV-2 de novo assembly.
 output:
   - meta:
       type: map

tests/software/pangolin/test.yml

@@ -4,4 +4,4 @@
     - pangolin
   files:
     - path: ./output/pangolin/test.pangolin.csv
-      md5sum: 1d513775cec0901ebee1359c91035d3a
+      md5sum: c8b1720f98c9e032908f61bbc05a0fe2

tests/software/spades/main.nf

@@ -8,9 +8,7 @@ workflow test_spades_single_end {
     input = [ [ id:'test', single_end:true ], // meta map
               [ file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-    coronaspades = false
+    SPADES ( input, [] )
-
-    SPADES ( input, [], coronaspades )
 }
 
 workflow test_spades_paired_end {
@@ -18,27 +16,6 @@ workflow test_spades_paired_end {
               [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
                 file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
             ]
-    coronaspades = false
 
-    SPADES ( input, [], coronaspades )
+    SPADES ( input, [] )
 }
-
-workflow test_coronospades_single_end {
-    input = [ [ id:'test', single_end:true ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
-            ]
-    coronaspades = true
-
-    SPADES ( input, [], coronaspades )
-}
-
-workflow test_coronospades_paired_end {
-    input = [ [ id:'test', single_end:false ], // meta map
-              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
-                file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
-            ]
-    coronaspades = true
-
-    SPADES ( input, [], coronaspades )
-}
-

tests/software/spades/test.yml

@@ -19,36 +19,7 @@
     - spades_paired_end
   files:
       - path: output/spades/test.assembly.gfa
-        md5sum: d546f9042f5ff911757e895e7b21f620
+        md5sum: faf76135ee390606b899c0197dc38e04
       - path: output/spades/test.contigs.fa
-        md5sum: f3e87d68521aa485d70aecd82de519b4
+        md5sum: 6148e25b33890c80f176f90f2dd88989
       - path: output/spades/test.spades.log
-
-- name: coronaspades single end
-  command: nextflow run ./tests/software/spades -entry test_coronospades_single_end -c tests/config/nextflow.config
-  tags:
-    - spades
-    - coronaspades_single_end
-  files:
-      - path: output/spades/test.assembly.gfa
-        md5sum: 46531ec9b845c1a1cb469627688fecb7
-      - path: output/spades/test.contigs.fa
-        md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
-      - path: output/spades/test.scaffolds.fa
-        md5sum: f2c4a48ebba560aa5c8fde04dbe905fc
-      - path: output/spades/test.gene_clusters.fa
-      - path: output/spades/test.spades.log
-
-- name: coronaspades paired end
-  command: nextflow run ./tests/software/spades -entry test_coronospades_paired_end -c tests/config/nextflow.config
-  tags:
-    - spades
-    - coronaspades_paired_end
-  files:
-      - path: output/spades/test.assembly.gfa
-        md5sum: d546f9042f5ff911757e895e7b21f620
-      - path: output/spades/test.contigs.fa
-        md5sum: f3e87d68521aa485d70aecd82de519b4
-      - path: output/spades/test.gene_clusters.fa
-      - path: output/spades/test.spades.log
-