Add dumpHashes in the debug profile

[maxulysse]

to have all possible hashes in the debug profile

PR checklist

• This comment contains a description of changes (with reason)
• CHANGELOG.md is updated
• If you've fixed a bug or added code that should be tested, add tests!
• Documentation in docs is updated

[maxulysse]

This is what we get on the terminal (for a single FASTQC process):

[04/63318d] process > fastqc:FASTQC (test) [100%] 1 of 1 ✔
[fastqc:FASTQC (test)] cache hash: 02f4c4991e915bf74d27dd709b66ebb2; mode: STANDARD; entries: 
  7433dca454178a3bc18c1a61439351b5 [java.util.UUID] b4920582-4452-4919-ae9f-b16377536302 
  125be3569cfa89fb6b4dd8abac71b2d5 [java.lang.String] fastqc:FASTQC 
  f0a03ba91e54c8b46bca83980e995469 [java.lang.String] def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
def rename_to = old_new_pairs*.join(' ').join(' ')
def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
"""
    printf "%s %s\\n" $rename_to | while read old_name new_name; do
        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
    done
    fastqc $args --threads $task.cpus $renamed_files

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
    END_VERSIONS
    """
 
  3d7e3f468681c009aabd42e495438f8e [java.lang.String] quay.io/biocontainers/fastqc:0.11.9--0 
  22a9e5e0e97f0475e310f04c56b1393a [java.lang.String] meta 
  b109ad80aeea270f1dc4ba3c4a4e295d [java.util.LinkedHashMap] [id:test, single_end:true] 
  553096c532e666fb42214fdf0520fe4a [java.lang.String] reads 
  b263454d0d36ccbf1fd22c9111e672e5 [nextflow.util.ArrayBag] [FileHolder(sourceObj:/[]/work/stage/b2/226e00b0ca64fdac3d519680a8bb54/test_1.fastq.gz, storePath:/[]/work/stage/b2/226e00b0ca64fdac3d519680a8bb54/test_1.fastq.gz, stageName:test_1.fastq.gz)] 
  4f9d4b0d22865056c37fb6d9c2a04a67 [java.lang.String] $ 
  16fe7483905cce7a85670e43e4678877 [java.lang.Boolean] true 
  7aa8f575a9dbd12c63a039cfee5205e2 [java.util.HashMap$EntrySet] [task.ext.args=null, task.cpus=2, task.ext.prefix=null, task.process=fastqc:FASTQC] 

[jfy133]

I would also have: cleanup = false

[codecov]

Codecov Report

Merging #2167 (1f30b40) into dev (27318f1) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##              dev    #2167   +/-   ##
=======================================
  Coverage   73.02%   73.02%           
=======================================
  Files          78       78           
  Lines        8384     8384           
=======================================
  Hits         6122     6122           
  Misses       2262     2262           

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[mirpedrol]

LGTM