Update samtools from 1.10 to 1.12 (#530)

* feat: remove social preview image to use GitHub OpenGraph

* feat: update samtools from 1.10 to 1.12

* fix: CI tests

* fix: add meta.yml file for samtools/merge

* Update software/samtools/merge/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update software/samtools/merge/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

software/samtools/faidx/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_FAIDX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
     }
 
     input:

software/samtools/flagstat/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_FLAGSTAT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
     }
 
     input:

software/samtools/idxstats/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_IDXSTATS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
     }
 
     input:

software/samtools/index/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_INDEX {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
     }
 
     input:

software/samtools/merge/main.nf

@@ -11,15 +11,15 @@ process SAMTOOLS_MERGE {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
     }
 
     input:
-    tuple val(meta),path(bams)
+    tuple val(meta), path(bams)
 
     output:
     tuple val(meta), path("*merged.bam"), emit: merged_bam

software/samtools/merge/meta.yml

@@ -0,0 +1,44 @@
+name: samtools_merge
+description: Merge BAM file
+keywords:
+    - merge
+    - bam
+    - sam
+    - cram
+tools:
+    - samtools:
+        description: |
+            SAMtools is a set of utilities for interacting with and post-processing
+            short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
+            These files are generated as output by short read aligners like BWA.
+        homepage: http://www.htslib.org/
+        documentation: hhttp://www.htslib.org/doc/samtools.html
+        doi: 10.1093/bioinformatics/btp352
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - bam:
+        type: file
+        description: BAM file
+        pattern: "*.{bam,cram,sam}"
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - merged_bam:
+        type: file
+        description: BAM file
+        pattern: "*.{bam}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@drpatelh"
+    - "@yuukiiwa "
+    - "@maxulysse"

software/samtools/mpileup/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_MPILEUP {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
     }
 
     input:

software/samtools/sort/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_SORT {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
     }
 
     input:

software/samtools/stats/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_STATS {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
     }
 
     input:

software/samtools/view/main.nf

@@ -11,11 +11,11 @@ process SAMTOOLS_VIEW {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
 
-    conda (params.enable_conda ? "bioconda::samtools=1.10" : null)
+    conda (params.enable_conda ? "bioconda::samtools=1.12" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/samtools:1.10--h9402c20_2"
+        container "https://depot.galaxyproject.org/singularity/samtools:1.12--hd5e65b6_0"
     } else {
-        container "quay.io/biocontainers/samtools:1.10--h9402c20_2"
+        container "quay.io/biocontainers/samtools:1.12--hd5e65b6_0"
     }
 
     input:

tests/software/samtools/flagstat/test.yml

@@ -4,5 +4,5 @@
     - samtools
     - samtools/flagstat
   files:
-    - path: ./output/samtools/test_paired_end.sorted.bam.flagstat
+    - path: ./output/samtools/test.paired_end.sorted.bam.flagstat
       md5sum: 6d7934c303b15ce473f64d502b79984e

tests/software/samtools/idxstats/test.yml

@@ -4,5 +4,5 @@
     - samtools
     - samtools/idxstats
   files:
-    - path: ./output/samtools/test_paired_end.sorted.bam.idxstats
+    - path: ./output/samtools/test.paired_end.sorted.bam.idxstats
       md5sum: df60a8c8d6621100d05178c93fb053a2

tests/software/samtools/index/test.yml

@@ -4,7 +4,7 @@
     - samtools
     - samtools/index
   files:
-    - path: output/samtools/test_paired_end.sorted.bam.bai
+    - path: output/samtools/test.paired_end.sorted.bam.bai
       md5sum: 704c10dd1326482448ca3073fdebc2f4
 
 - name: samtools index csi
@@ -13,5 +13,5 @@
     - samtools
     - samtools/index
   files:
-    - path: output/samtools/test_paired_end.sorted.bam.csi
+    - path: output/samtools/test.paired_end.sorted.bam.csi
       md5sum: 3dd9e3ed959fca075b88bb8dc3cf7dbd

tests/software/samtools/merge/main.nf

@@ -6,7 +6,7 @@ include { SAMTOOLS_MERGE } from '../../../../software/samtools/merge/main.nf' ad
 
 workflow test_samtools_merge {
     input = [ [ id: 'test' ], // meta map
-               [ file(params.test_data['sarscov2']['illumina']['test_methylated_paired_end_sorted_bam'], checkIfExists: true),
+               [ file(params.test_data['sarscov2']['illumina']['test_paired_end_methylated_sorted_bam'], checkIfExists: true),
                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
                  file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)]
                ]

tests/software/samtools/mpileup/main.nf

@@ -8,7 +8,7 @@ workflow test_samtools_mpileup {
     input = [ [ id:'test', single_end:false ], // meta map
                 file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
             ]
-    fasta = file("${launchDir}/tests/data/genomics/sarscov2/genome/genome.fasta", checkIfExists: true)
+    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
     SAMTOOLS_MPILEUP ( input, fasta )
 }

tests/software/samtools/mpileup/test.yml

@@ -5,4 +5,4 @@
     - samtools/mpileup
   files:
     - path: ./output/samtools/test.mpileup
-      md5sum: 56c4cd5a4ecb7d6364878818f46ae256
+      md5sum: 3608af83ffe3efbb1337f0ffb205337d

tests/software/samtools/sort/test.yml

@@ -5,4 +5,4 @@
     - samtools/sort
   files:
     - path: output/samtools/test.bam
-      md5sum: 7e32f47768f922a73ccec4dc24db1973
+      md5sum: 3997667dee6b45d682865c6bf82d0378

tests/software/samtools/stats/test.yml

@@ -4,5 +4,5 @@
     - samtools
     - samtools/stats
   files:
-    - path: ./output/samtools/test_paired_end.sorted.bam.stats
-      md5sum: 5f12c46ae4491b48611194c94093ebfb
+    - path: ./output/samtools/test.paired_end.sorted.bam.stats
+      md5sum: 95f7edae5d02c10c4004d9ab1d7d8ef3