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Merged
BenjaminWehnert1008 merged 9 commits into from
Apr 7, 2026
Merged

centralising container links and integrate mutscan for fitness calculation #41

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2ee08eb
centralising container links and integrate mutscan for fitness calcul…
BenjaminWehnert1008 Mar 20, 2026
6836685
AMD/ARM compatability and updated test snapshot
BenjaminWehnert1008 Mar 20, 2026
cb69845
testing ...
BenjaminWehnert1008 Mar 20, 2026
1a70ba3
fix containers
BenjaminWehnert1008 Mar 20, 2026
33b20a8
updated conatiner structure and DiMSum now also working on ARM
BenjaminWehnert1008 Mar 21, 2026
ca01350
new metro
BenjaminWehnert1008 Mar 21, 2026
2dbffe4
new metro as png...
BenjaminWehnert1008 Mar 21, 2026
8213b27
fixed metro
BenjaminWehnert1008 Mar 21, 2026
44dba03
pipeline metro typo
BenjaminWehnert1008 Mar 25, 2026
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8 changes: 8 additions & 0 deletions conf/modules.config
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Expand Up @@ -179,4 +179,12 @@ process {
saveAs: { filename -> filename == 'versions.yml' ? null : filename }
]
}

withName: 'RUN_MUTSCAN' {
publishDir = [
path: "${params.outdir}/fitness/mutscan_results",
mode: 'copy',
saveAs: { filename -> filename == 'versions.yml' ? null : filename }
]
}
}
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@MaximilianStammnitz MaximilianStammnitz Mar 21, 2026

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looks awesome – only need to flip colours between pink & orange in the legend

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@BenjaminWehnert1008 BenjaminWehnert1008 Mar 21, 2026

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damn it, sure!

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5 changes: 3 additions & 2 deletions modules/local/dmsanalysis/aa_seq/main.nf
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Expand Up @@ -3,9 +3,10 @@ process DMSANALYSIS_AASEQ {
label 'process_single'

conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

input:
tuple val(meta), path(wt_seq)
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4 changes: 2 additions & 2 deletions modules/local/dmsanalysis/possible_mutations/main.nf
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Expand Up @@ -5,8 +5,8 @@ process DMSANALYSIS_POSSIBLE_MUTATIONS {
conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

input:
tuple val(meta), path(wt_seq)
Expand Down
5 changes: 3 additions & 2 deletions modules/local/dmsanalysis/process_gatk/main.nf
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Expand Up @@ -3,9 +3,10 @@ process DMSANALYSIS_PROCESS_GATK {
label 'process_single'

conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

publishDir "${params.outdir}/intermediate_files", mode: 'copy'

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5 changes: 3 additions & 2 deletions modules/local/fitness/find_synonymous_mutation/main.nf
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Expand Up @@ -3,9 +3,10 @@ process FIND_SYNONYMOUS_MUTATION {
label 'process_single'

conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

input:
tuple val(sample), path(counts_merged) // from MERGE_COUNTS.out.merged_counts
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5 changes: 3 additions & 2 deletions modules/local/fitness/fitness_QC/main.nf
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Expand Up @@ -3,9 +3,10 @@ process FITNESS_QC {
label 'process_single'

conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

input:
tuple val(sample), path(fitness_estimation_tsv) // from FITNESS_CALCULATION
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5 changes: 3 additions & 2 deletions modules/local/fitness/fitness_calculation/main.nf
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Expand Up @@ -3,9 +3,10 @@ process FITNESS_CALCULATION {
label 'process_single'

conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

input:
tuple val(sample), path(counts_merged)
Expand Down
5 changes: 3 additions & 2 deletions modules/local/fitness/fitness_experimental_design/main.nf
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Expand Up @@ -3,9 +3,10 @@ process EXPDESIGN_FITNESS {
label 'process_single'

conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

input:
path samplesheet_csv
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5 changes: 3 additions & 2 deletions modules/local/fitness/fitness_heatmap/main.nf
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Expand Up @@ -3,9 +3,10 @@ process FITNESS_HEATMAP {
label 'process_single'

conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

input:
tuple val(sample), path(fitness_estimation_tsv) // from FITNESS_CALCULATION
Expand Down
5 changes: 3 additions & 2 deletions modules/local/fitness/merge_counts/main.nf
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Expand Up @@ -3,9 +3,10 @@ process MERGE_COUNTS {
label 'process_single'

conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:ce2ba7ad7f6e7f2c'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-base_r-biocmanager_r-dplyr_pruned:0fd2e39a5bf2ecaa' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

input:
tuple val(sample), val(metas), path(input_counts), path(output_counts)
Expand Down
5 changes: 0 additions & 5 deletions modules/local/fitness/merge_counts/templates/merge_counts.R
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Expand Up @@ -4,13 +4,9 @@
# 1. SETUP & INPUTS
# --------------------------------------------------------------

# Nextflow übergibt Listen von Dateien (path input_counts) als
# leerzeichengetrennten String (z.B. "file1 file2 file3").
# Wir lesen diese Strings ein:
raw_inputs_str <- "$input_counts"
raw_outputs_str <- "$output_counts"

# Funktion zum Splitten des Strings in einen Vektor
parse_paths <- function(x) {
if (x == "" || x == "[]") return(character(0))
# Split at spaces
Expand Down Expand Up @@ -60,7 +56,6 @@ col_names <- c(
)

# Initialize dataframe with 0 counts
# Wir nutzen matrix initialization für Performance
out <- data.frame(
nt_seq = all_seqs,
matrix(0, nrow = length(all_seqs), ncol = n_in + n_out),
Expand Down
4 changes: 2 additions & 2 deletions modules/local/fitness/run_dimsum/main.nf
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Expand Up @@ -4,8 +4,8 @@ process RUN_DIMSUM {

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity'
? 'oras://community.wave.seqera.io/library/r-dimsum:1.4--4357734d345c8ccc'
: 'docker.io/bwehnert1008/dms_qc_dimsum_environment@sha256:08f3bd8441df7b4a7e05aadeca178862153cf723e64097a48a2744b2698b15dd' }"
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/9298c391f285d7f2c1155f6a519a96c4f7591971780ba4f10569558282f40b6f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_r-dimsum_r-base_r-data.table_pruned:cca13eed371a9d84' }"

input:
tuple val(sample), path(counts_merged)
Expand Down
7 changes: 7 additions & 0 deletions modules/local/fitness/run_mutscan/environment.yml
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@@ -0,0 +1,7 @@
channels:
- conda-forge
- bioconda
dependencies:
- bioconda::bioconductor-biostrings=2.74.0
- bioconda::bioconductor-mutscan=1.0.0
- conda-forge::r-base=4.4.1
24 changes: 24 additions & 0 deletions modules/local/fitness/run_mutscan/main.nf
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@@ -0,0 +1,24 @@
process RUN_MUTSCAN {
tag "${sample.sample}"
label 'process_medium'

conda "${moduleDir}/environment.yml"

container "${ workflow.containerEngine == 'singularity'
? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/73/73a72ec77725aeb67678a74228938fdd6827b669d01a8c96951b1a8ef96eeb0f/data'
: 'community.wave.seqera.io/library/bioconductor-biostrings_bioconductor-mutscan_r-base_r-biocmanager_pruned:c65036d76406f342' }"

input:
tuple val(sample), path(counts_merged)
path(syn_wt_txt)
path(exp_design)

output:
tuple val(sample), path("fitness_estimation_mutscan_edgeR.tsv"), emit: fitness_mutscan_edgeR
tuple val(sample), path("fitness_estimation_mutscan_limma.tsv"), emit: fitness_mutscan_limma
tuple val(sample), path("*.pdf"), emit: qc_plots
path "versions.yml", emit: versions

script:
template 'fitness_calculation_mutscan.R'
}
1 change: 0 additions & 1 deletion modules/local/fitness/run_mutscan/readme.md
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