remove soft-linking of fasta instead stage in dir (#7081)

* remove soft-linking of fasta instead stage in dir * add comments for fasta stageAs
nf-core · Nov 26, 2024 · 7992214 · 7992214
1 parent 426f3c8
commit 7992214
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Showing 7 changed files with 23 additions and 29 deletions.
diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf
@@ -9,7 +9,7 @@ process BISMARK_ALIGN {
 
     input:
     tuple val(meta), path(reads)
-    tuple val(meta2), path(fasta)
+    tuple val(meta2), path(fasta, stageAs: 'tmp/*') // This change mounts as directory containing the FASTA file to prevent nested symlinks
     tuple val(meta3), path(index)
 
     output:
@@ -56,13 +56,11 @@ process BISMARK_ALIGN {
         }
     }
     """
-    ln -sf \$(readlink $fasta) $index/$fasta
-
     bismark \\
-        $fastq \\
-        --genome $index \\
+        ${fastq} \\
+        --genome ${index} \\
         --bam \\
-        $args
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bismark/coverage2cytosine/main.nf b/modules/nf-core/bismark/coverage2cytosine/main.nf
@@ -9,7 +9,7 @@ process BISMARK_COVERAGE2CYTOSINE {
 
     input:
     tuple val(meta), path(coverage_file)
-    tuple val(meta2), path(fasta)
+    tuple val(meta2), path(fasta, stageAs: 'tmp/*') // This change mounts as directory containing the FASTA file to prevent nested symlinks
     tuple val(meta3), path(index)
 
     output:
@@ -25,16 +25,12 @@ process BISMARK_COVERAGE2CYTOSINE {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    if [ ! -f $index/$fasta ]; then
-        ln -s \$(readlink $fasta) $index/$fasta;
-    fi
-
     coverage2cytosine \\
-        $coverage_file \\
-        --genome $index \\
+        ${coverage_file} \\
+        --genome ${index} \\
         --output ${prefix} \\
         --gzip \\
-        $args
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf
@@ -24,9 +24,9 @@ process BISMARK_DEDUPLICATE {
     def seqtype = meta.single_end ? '-s' : '-p'
     """
     deduplicate_bismark \\
-        $args \\
-        $seqtype \\
-        --bam $bam
+        ${args} \\
+        ${seqtype} \\
+        --bam ${bam}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf
@@ -21,11 +21,9 @@ process BISMARK_GENOMEPREPARATION {
     def args = task.ext.args ?: ''
     """
     bismark_genome_preparation \\
-        $args \\
+        ${args} \\
         BismarkIndex
 
-    rm $fasta
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//')

diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap
@@ -102,7 +102,8 @@
                                     "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6",
                                     "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59"
                                 ]
-                            ]
+                            ],
+                            "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
                         ]
                     ]
                 ],
@@ -134,7 +135,8 @@
                                     "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6",
                                     "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59"
                                 ]
-                            ]
+                            ],
+                            "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6"
                         ]
                     ]
                 ],
@@ -144,9 +146,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.1"
         },
-        "timestamp": "2024-10-13T08:26:20.352083082"
+        "timestamp": "2024-11-25T15:32:55.125985002"
     }
 }
diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf
@@ -36,13 +36,13 @@ process BISMARK_METHYLATIONEXTRACTOR {
     def seqtype  = meta.single_end ? '-s' : '-p'
     """
     bismark_methylation_extractor \\
-        $bam \\
+        ${bam} \\
         --bedGraph \\
         --counts \\
         --gzip \\
         --report \\
-        $seqtype \\
-        $args
+        ${seqtype} \\
+        ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf
@@ -20,7 +20,7 @@ process BISMARK_REPORT {
     script:
     def args = task.ext.args ?: ''
     """
-    bismark2report $args
+    bismark2report ${args}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":