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Feature/core cutadapt #71

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48f5735
Major initial push to use nf-core cutadapt; requires some additional …
cjfields Nov 17, 2025
e124937
bump multiqc to latest
cjfields Nov 18, 2025
950113d
bump multiqc to latest
cjfields Nov 18, 2025
4574483
convert pacbio workflow over for cutadapt
cjfields Nov 18, 2025
6ae8d1f
start removing unused params
cjfields Nov 18, 2025
6f6758f
get pacbio working, fix read tracking, and also adjust filterAndTrim …
cjfields Nov 19, 2025
efb51a0
update nf-core modules
cjfields Nov 19, 2025
e3a5dd1
update nf-core modules
cjfields Nov 19, 2025
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61 changes: 49 additions & 12 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,7 @@ process {
}

withName: OVERLAP_HEATMAP {

publishDir = [
[
path: { "${params.outdir}/TADA/QC/Plots/" },
Expand Down Expand Up @@ -65,18 +66,54 @@ process {
]
}

withName: ILLUMINA_CUTADAPT {
publishDir = [
path: { "${params.outdir}/Intermediate/cutadapt" },
mode: params.publish_dir_mode
]
}

withName: PACBIO_CUTADAPT {
publishDir = [
path: { "${params.outdir}/Intermediate/cutadapt" },
mode: params.publish_dir_mode
]
withName: SHORT_READ_CUTADAPT {
ext.args = { [
// TODO: not sure why this one is being weird, but
// seems to trigger an error even though this is
// cutadapt 5.0
// "--json=${meta.id}.cutadapt.json",
params.cutadapt_strict_match ? "--pair-filter=any" : "--pair-filter=both",
"--report=minimal",
"--max-ee ${[params.maxEE_for,params.maxEE_rev].max()}",
params.trunc_for > 0 ? "-l ${params.trunc_for}" : "",
params.maxN >= 0 ? "--max-n ${params.maxN}" : "",
params.min_read_len ? "-m ${params.min_read_len}" : "-m 50",
params.max_read_len != "Inf" ? "-M ${params.max_read_len}" : "",
!meta.single_end && params.trunc_rev > 0 ? "-L ${params.trunc_rev}" : "",
params.illumina_twocolor ? "--nextseq-trim=2" : "",
"-g ${meta.for}",
params.cutadapt_dovetail ? "-a ${meta.rev_rc} -n 2" : "",
meta.single_end ? "" : "-G ${meta.rev}",
!meta.single_end && params.cutadapt_dovetail ? "-A ${meta.for_rc}" : "",
].join(' ').trim() }
ext.prefix = { "${meta.id}" }
publishDir = [
path: { "${params.outdir}/Intermediate/cutadapt" },
mode: params.publish_dir_mode
]
}

withName: LONG_READ_CUTADAPT {
ext.args = { [
// TODO: not sure why this one is being weird, but
// seems to trigger an error even though this is
// cutadapt 5.0
// "--json=${meta.id}.cutadapt.json",
"--rc",
"--report=minimal",
"--max-ee ${[params.maxEE_for,params.maxEE_rev].max()}",
// params.trunc_for > 0 ? "-l ${params.trunc_for}" : "",
params.cutadapt_strict_match ? "-g ${meta.for}...${meta.rev_rc}" : "-a ${for_primer}...${rev_primer_rc}",
params.maxN >= 0 ? "--max-n ${params.maxN}" : "",
params.min_read_len ? "-m ${params.min_read_len}" : "-m 50",
params.max_read_len != "Inf" ? "-M ${params.max_read_len}" : "",
"--untrimmed-output ${meta.id}.untrimmed.fastq.gz",
].join(' ').trim() }
ext.prefix = { "${meta.id}" }
publishDir = [
path: { "${params.outdir}/Intermediate/cutadapt" },
mode: params.publish_dir_mode
]
}

withName: ILLUMINA_DADA2_FILTER_AND_TRIM {
Expand Down
28 changes: 14 additions & 14 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,72 +7,72 @@
"nf-core": {
"cutadapt": {
"branch": "master",
"git_sha": "003920c7f9a8ae19b69a97171922880220bedf56",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "b1966f36ec9de31927b2603d8f499960b2a4c294",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"fasttree": {
"branch": "master",
"git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"mafft/align": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
},
"mmseqs/createdb": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"git_sha": "38697a933bef7041bb935c9b8374d9948ce6c794",
"installed_by": ["modules"]
},
"mmseqs/createindex": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "38697a933bef7041bb935c9b8374d9948ce6c794",
"installed_by": ["modules"]
},
"mmseqs/createtsv": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
},
"mmseqs/easysearch": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"git_sha": "38697a933bef7041bb935c9b8374d9948ce6c794",
"installed_by": ["modules"]
},
"mmseqs/search": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"git_sha": "38697a933bef7041bb935c9b8374d9948ce6c794",
"installed_by": ["modules"]
},
"mmseqs/taxonomy": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
},
"mmseqs/tsv2exprofiledb": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
},
"multiqc": {
"branch": "master",
"git_sha": "7b50cb7be890e4b28cffb82e438cc6a8d7805d3f",
"git_sha": "82a79183037a403ad1b6714e5dbcff25500efaf6",
"installed_by": ["modules"]
},
"muscle": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
},
"muscle5/super5": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"installed_by": ["modules"]
}
}
Expand Down
2 changes: 1 addition & 1 deletion modules/local/dadainfer.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -66,7 +66,7 @@ process DADA2_POOLED_INFER {

tracking_dds <- as.data.frame(sapply(dds, getN))
colnames(tracking_dds) <- c("dada2.denoised.pooled.${readmode}")
nms <- gsub(".R[12].filtered.fastq.gz", "", rownames(tracking_dds))
nms <- gsub("(.R[12])?.trim.fastq.gz", "", rownames(tracking_dds))
tracking_dds <- tracking_dds %>%
as_tibble() %>%
mutate(SampleID = nms, .before = 1)
Expand Down
213 changes: 0 additions & 213 deletions modules/local/filterandtrim.nf
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