Read coverage review

modules.json

@@ -45,11 +45,6 @@
                         "git_sha": "72e277acfd9e61a9f1368eafb4a9e83f5bcaa9f5",
                         "installed_by": ["modules"]
                     },
-                    "samtools/faidx": {
-                        "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
-                    },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",

modules/local/blobtk_depth.nf

@@ -8,7 +8,7 @@ process BLOBTK_DEPTH {
     container "docker.io/genomehubs/blobtk:0.6.5"
 
     input:
-    tuple val(meta), path(cram), path(bai)
+    tuple val(meta), path(bam), path(bai)
 
     output:
     tuple val(meta), path('*.coverage.bedGraph')    , emit: bedgraph
@@ -22,7 +22,7 @@ process BLOBTK_DEPTH {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     blobtk depth \\
-        -c ${cram} \\
+        -b ${bam} \\
         $args \\
         -O ${prefix}.coverage.bedGraph \\
 

modules/local/change_name.nf

@@ -1,43 +1,26 @@
 process CHANGE_NAME {
     tag "$meta.id"
-    label 'process_single'
-
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
-        'docker.io/ubuntu:20.04' }"
+    executor 'local'
 
     input:
     tuple val(meta), path(file)
 
     output:
     tuple val(meta), path("*.${file.extension}"), emit: file
-    path "versions.yml", emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     def prefix = task.ext.prefix ?: "${meta.id}"
     def new_fn = "${prefix}.${file.extension}"
     """
-    ln -s ${file} ${new_fn}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        coreutils: $VERSION
-    END_VERSIONS
+    ln -sf ${file} ${new_fn}
     """
 
     stub:
-    def VERSION = "9.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${new_fn}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        coreutils: $VERSION
-    END_VERSIONS
     """
 }