Nextflow Modules
Showing module(s) with keyword "merge"
| Module | Keywords | Description |
|---|---|---|
| nf-core/agat/spmergeannotations | genomics gff merge combine | This script merge different gff annotation files in one. It uses the AGAT parser that takes care of duplicated names and fixes other oddities met in those files. |
| nf-core/atlas/splitmerge | split merge bam read group | split single end read groups by length and merge paired end reads |
| nf-core/bcftools/merge | variant calling merge VCF | Merge VCF files |
| nf-core/bedtools/merge | bed merge bedtools overlapped bed | combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. |
| nf-core/biobambam/bammerge | merge bam sorted | Merge a list of sorted bam files |
| nf-core/concoct/extractfastabins | contigs fragment mags binning fasta cut cut up bins merge | Creates a FASTA file for each new cluster assigned by CONCOCT |
| nf-core/concoct/mergecutupclustering | contigs fragment mags binning fasta cut cut up merge | Merge consecutive parts of the original contigs original cut up by cut_up_fasta.py |
| nf-core/cooler/merge | merge cooler hic | Merge multiple coolers with identical axes |
| nf-core/custom/orfmerge | orf ribo-seq catalogue merge clustering | Cluster normalised per-sample, per-caller ORF predictions into a single cohort-level catalogue. Pair with `custom/orfnormalise` upstream and (typically) `bedtools/getfasta` + `seqkit/translate` downstream to obtain the AA FASTA. Strategy is class-aware (operating on the harmonised `orf_class` written by `custom/orfnormalise`): - canonical_cds: collapse by (transcript_id, strand). One canonical CDS per transcript by definition. - uORF, dORF, other: collapse by (transcript_id, strand, start, end). A single transcript can host multiple distinct uORFs / dORFs / internal ORFs, so keying on the outer span keeps them in separate clusters while still merging cross-caller calls that agree on coordinates. - novel_u, smORF: greedy reciprocal-overlap clustering on the outer genomic span at `--reciprocal-overlap` (default 0.8). Catches fuzzy cross-caller matches and exact-coordinate collapses in one pass. Order-dependent at the boundary: a chain A-B-C where A-B and B-C overlap at ~0.85 but A-C only at ~0.75 may cluster as {A,B,C} or {A,B}+{C} depending on iteration order. Rare in practice at 0.8. Cross-caller consensus is recorded in two column families on the catalogue TSV: - `called_by_<caller>`: 0/1 indicator per supported caller (ribotish, ribocode, ribotricer, rpbp, price). - `score_<caller>`: best score from that caller within the cluster. Score direction is per-caller (p-values are minimised; Bayes factors / phase scores are maximised). Cross-sample recurrence is recorded in two further columns: - `n_samples`: number of distinct samples contributing to the cluster (a cohort recurrence metric). - `samples`: sorted, comma-separated list of those sample ids. Emits a small MultiQC custom-content TSV (per-class counts) for inclusion in downstream MultiQC reports. |
| nf-core/custom/rsemmergecounts | rsem merge counts gene expression | Merge per-sample RSEM results into wide and long format TSV matrices |
| nf-core/elprep/merge | bam sam merge | Merge split bam/sam chunks in one file |
| nf-core/expansionhunterdenovo/merge | expansionhunterdenovo merge str | Merge STR profiles into a multi-sample STR profile |
| nf-core/fastk/merge | merge k-mer histogram fastk | A tool to merge FastK histograms |
| nf-core/fgumi/merge | merge bam alignment sort | Merge pre-sorted BAM files into a single sorted BAM |
| nf-core/gatk4/mergebamalignment | alignment bam gatk4 merge mergebamalignment | Merge unmapped with mapped BAM files |
| nf-core/gatk4/mergemutectstats | gatk4 merge mutect2 mutectstats | Merges mutect2 stats generated on different intervals/regions |
| nf-core/gatk4/mergevcfs | gatk4 merge vcf | Merges several vcf files |
| nf-core/gatk4/splitncigarreads | gatk4 merge vcf | Splits reads that contain Ns in their cigar string |
| nf-core/gffcompare | transcripts gtf merge compare | Compare, merge, annotate and estimate accuracy of generated gtf files |