Updated file structure for local processes

[BenjaminWehnert1008]

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• This comment contains a description of changes (with reason).
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[BenjaminWehnert1008]

As discussed, each process is now organized into its own module. @mashehu, is this now in line with the nf-core standards?

I'm now seeing some redundant terminal output (FastQC being printed multiple times) during the setup phase. Since the pipeline runs without errors, I'm not sure if this is relevant...

[-        ] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC                              -
executor >  local (1)
[-        ] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC                              | 0 of 3
executor >  local (1)
[-        ] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC                              | 0 of 4
executor >  local (2)
[-        ] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC                              | 0 of 4
executor >  local (2)
[-        ] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC                              | 0 of 4
executor >  local (3)
[-        ] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC                              | 0 of 4
executor >  local (4)
[-        ] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC                              | 0 of 4
executor >  local (5)
[4a/a56925] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC (GID1A_input_2_pe)           | 0 of 4
executor >  local (5)
[4a/a56925] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC (GID1A_input_2_pe)           | 0 of 4
executor >  local (6)
[4a/a56925] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC (GID1A_input_2_pe)           | 1 of 4
executor >  local (62)
[98/283f4a] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:FASTQC (GID1A_output_1_pe)          | 4 of 4 ✔
[9f/f751f1] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:MULTIQC                             | 1 of 1 ✔
[d8/dad3a5] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:BWA_INDEX (GID1A.fasta)             | 1 of 1 ✔
[72/2dc070] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:BWA_MEM (GID1A_input_2_pe)          | 4 of 4 ✔
[68/297f90] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:BAMFILTER_DMS (GID1A_input_2_pe)    | 4 of 4 ✔
[59/5cee1c] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:PREMERGE (GID1A_input_2_pe)         | 4 of 4 ✔
[c5/29faaf] NFC…SCAN:DEEPMUTSCAN:GATK_SATURATIONMUTAGENESIS (GID1A_input_2_pe) | 4 of 4 ✔
[43/eb9558] NFC…EEPMUTSCAN:DEEPMUTSCAN:DMSANALYSIS_AASEQ (amino_acid_sequence) | 1 of 1 ✔
[40/471e48] NFC…MSANALYSIS_POSSIBLE_MUTATIONS (table /w all possible variants) | 1 of 1 ✔
[2e/421a9e] NFC…UTSCAN:DEEPMUTSCAN:DMSANALYSIS_PROCESS_GATK (GID1A_input_2_pe) | 4 of 4 ✔
[37/af0b0d] NFC…AN:DEEPMUTSCAN:VISUALIZATION_COUNTS_PER_COV (GID1A_input_2_pe) | 4 of 4 ✔
[54/0ce69c] NFC…AN:DEEPMUTSCAN:VISUALIZATION_COUNTS_HEATMAP (GID1A_input_2_pe) | 4 of 4 ✔
[62/6e569c] NFC…SCAN:VISUALIZATION_GLOBAL_POS_BIASES_COUNTS (GID1A_input_2_pe) | 4 of 4 ✔
[2b/248f3e] NFC…MUTSCAN:VISUALIZATION_GLOBAL_POS_BIASES_COV (GID1A_input_2_pe) | 4 of 4 ✔
[66/1900f2] NFC…EPMUTSCAN:DEEPMUTSCAN:VISUALIZATION_LOGDIFF (GID1A_input_2_pe) | 4 of 4 ✔
[f3/8a5060] NFC…PMUTSCAN:DEEPMUTSCAN:VISUALIZATION_SEQDEPTH (GID1A_input_2_pe) | 4 of 4 ✔
[88/4c798c] NFC…_DEEPMUTSCAN:DEEPMUTSCAN:GATK_GATKTOFITNESS (GID1A_input_2_pe) | 4 of 4 ✔
[d4/c4a82b] NFC…_DEEPMUTSCAN:DEEPMUTSCAN:CALCULATEFITNESS:MERGE_COUNTS (GID1A) | 1 of 1 ✔
[50/87aa8c] NFC…UTSCAN:CALCULATEFITNESS:EXPDESIGN_FITNESS (experimentalDesign) | 1 of 1 ✔
[5d/b6553e] NFC…:DEEPMUTSCAN:CALCULATEFITNESS:FIND_SYNONYMOUS_MUTATION (GID1A) | 1 of 1 ✔
[24/aa28da] NFC…TSCAN:DEEPMUTSCAN:CALCULATEFITNESS:FITNESS_CALCULATION (GID1A) | 1 of 1 ✔
[b5/3b803c] NFCORE_DEEPMUTSCAN:DEEPMUTSCAN:CALCULATEFITNESS:FITNESS_QC (GID1A) | 1 of 1 ✔
[2f/0d8e64] NFC…EEPMUTSCAN:DEEPMUTSCAN:CALCULATEFITNESS:FITNESS_HEATMAP (null) | 1 of 1 ✔
-[nf-core/deepmutscan] Pipeline completed successfully-
Completed at: 10-Mar-2026 18:26:54
Duration    : 5m 21s
CPU hours   : 0.3
Succeeded   : 62

[mashehu]

@nf-core-bot fix linting

[BenjaminWehnert1008]

@mashehu I think you mentioned better not to use underscores. Looking at the names of the updated local module folders, would this still be okay? I noticed that some other pipelines do it similarly (e.g. https://github.com/nf-core/rnaseq/tree/3.23.0/modules/local/deseq2_qc)

[mashehu]

for local modules it matters less, and if the linter is happy, it's fine.