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Updates to changelog and removing CHUNKFASTA, replaced with seqkit
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@DLBPointon
DLBPointon committed Nov 26, 2024
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72 changes: 38 additions & 34 deletions CHANGELOG.md
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Expand Up @@ -20,6 +20,9 @@ Our 3rd release for sanger-tol/treeval.
- Adding arch specification to Pretext GitHub actions runner. Hopefully this will stop the spurious errors we see on there.
- Addition of steps into schema.
- Adds \*ktab as an output.
- Updated singularity containers
- Added `--metaeuk` to BUSCO_BUSCO, default was causing pipeline errors on Actions -- Needs more investigation.
- Replaced Pyfasta split (depreciated 6 years ago) with Seqkit split which is frequently updated and very fast.

### Parameters

Expand All @@ -31,40 +34,41 @@ Our 3rd release for sanger-tol/treeval.

Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

| Module | Old Version | New Versions |
| -------------------------------------- | ---------------- | ------------ |
| bamtobed_sort ( bedtools + samtools ) | 2.31.0 + 1.17 | |
| bedtools | 2.31.1 | - |
| busco\* | 5.5.0 | - |
| bwa-mem2 | 2.2.1 | |
| cat | 2.3.4 | |
| chunk_fasta ( pyfasta ) | 0.5.2-1 | |
| cooler | 0.9.2 | |
| cram_filter_align_bwamem2_fixmate_sort | - | |
| ^ ( samtools + bwamem2 ) ^ | 1.17 + 2.2.1 | |
| coreutils | 9.1 | |
| fastk | 1.0.1 | |
| gcc | 10.4.0 | |
| find_telomere_windows ( java-jdk ) | 8.0.112 | |
| generate_cram_csv ( samtools ) | 1.17 | |
| gnu-sort | 8.25 | 9.3 |
| juicer_tools_pre ( java-jdk ) | 8.0.112 | |
| perl | 5.26.2 | |
| merquryfk | 1.0.1 | |
| minimap2 + samtools | 2.24 + 1.14 | |
| minimap2_index | 2.24 | 2.28 |
| miniprot | 0.11--he4a0461_2 | |
| mummer | 3.23 | |
| paftools ( minimap2 + samtools ) | 2.24 + 1.14 | |
| pretextmap + samtools | 0.0.2 + 1.17 | 0.0.3 + 1.17 |
| python | 3.9 | - |
| - pandas | 1.5.2 | - |
| samtools | 1.18 | 1.21 |
| selfcomp_splitfasta ( perl-bioperl ) | 1.7.8-1 | |
| seqtk | 1.4 | |
| tabix | 1.11 | |
| ucsc | 377 | 447 |
| windowmasker (blast) | 2.14.0 | 2.15.0 |
| Module | Old Version | New Versions |
| -------------------------------------- | ---------------- | ----------------- |
| bamtobed_sort ( bedtools + samtools ) | 2.31.0 + 1.17 | |
| bedtools | 2.31.1 | - |
| busco\* | 5.5.0 | - |
| bwa-mem2 | 2.2.1 | |
| cat | 2.3.4 | |
| chunk_fasta ( pyfasta ) | 0.5.2-1 | REMOVED |
| cooler | 0.9.2 | |
| cram_filter_align_bwamem2_fixmate_sort | - | |
| ^ ( samtools + bwamem2 ) ^ | 1.17 + 2.2.1 | |
| coreutils | 9.1 | |
| fastk | 1.0.1 | |
| gcc | 10.4.0 | |
| find_telomere_windows ( java-jdk ) | 8.0.112 | |
| generate_cram_csv ( samtools ) | 1.17 | |
| gnu-sort | 8.25 | 9.3 |
| juicer_tools_pre ( java-jdk ) | 8.0.112 | |
| perl | 5.26.2 | |
| merquryfk | 1.0.1 | |
| minimap2 + samtools | 2.24 + 1.14 | |
| minimap2_index | 2.24 | 2.28 |
| miniprot | 0.11--he4a0461_2 | |
| mummer | 3.23 | |
| paftools ( minimap2 + samtools ) | 2.24 + 1.14 | |
| pretextmap + samtools | 0.0.2 + 1.17 | 0.0.3 + 1.17 |
| python | 3.9 | - |
| - pandas | 1.5.2 | - |
| samtools | 1.18 | 1.21 |
| selfcomp_splitfasta ( perl-bioperl ) | 1.7.8-1 | |
| seqtk | 1.4 | |
| seqkit | ADDED | 2.9.0--h9ee0642_0 |
| tabix | 1.11 | |
| ucsc | 377 | 447 |
| windowmasker (blast) | 2.14.0 | 2.15.0 |

- busco is currently pinned to v5.5.0 - Upgrading v5.7.1 would cause github actions to crash. Further investigation needed.

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48 changes: 0 additions & 48 deletions modules/local/chunkfasta.nf
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13 changes: 6 additions & 7 deletions subworkflows/local/selfcomp.nf
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Expand Up @@ -12,7 +12,7 @@ include { BEDTOOLS_SORT } from '../../modules/nf-core/bedtools/
include { SELFCOMP_SPLITFASTA } from '../../modules/local/selfcomp_splitfasta'
include { SELFCOMP_MUMMER2BED } from '../../modules/local/selfcomp_mummer2bed'
include { SELFCOMP_MAPIDS } from '../../modules/local/selfcomp_mapids'
include { CHUNKFASTA } from '../../modules/local/chunkfasta'
include { SEQKIT_SPLIT } from '../../modules/local/seqkit/split/main'
include { CAT_CAT } from '../../modules/nf-core/cat/cat/main'
include { SELFCOMP_ALIGNMENTBLOCKS } from '../../modules/local/selfcomp_alignmentblocks'
include { CONCATBLOCKS } from '../../modules/local/concatblocks'
Expand Down Expand Up @@ -57,28 +57,28 @@ workflow SELFCOMP {
// MODULE: SPLIT REFERENCE FILE INTO 1GB CHUNKS
// THIS IS THE QUERY, AND REFERENCE IF GENOME.size() > 1GB
//
CHUNKFASTA(
SEQKIT_SPLIT(
SELFCOMP_SPLITFASTA.out.fa,
chunk_number
)
ch_versions = ch_versions.mix(CHUNKFASTA.out.versions)
ch_versions = ch_versions.mix(SEQKIT_SPLIT.out.versions)

//
// LOGIC: STRIP META FROM QUERY, AND COMBINE WITH REFERENCE FILE
// THIS LEAVES US WITH n=( REFERENCE + QUERY) IF GENOME.SIZE() < 1GB
// OR n=((REFERENCE / 1E9) * (REFENCE / 1E9)) IF GENOME.SIZE() > 1GB
//
CHUNKFASTA.out.fasta
SEQKIT_SPLIT.out.fasta
.map{meta, query ->
query
}
.collect() // Collect any output from CHUNKFASTA
.collect() // Collect any output from SEQKIT_SPLIT
.map {it ->
tuple( [ len: it.size() ], // Calc length of list
it
)
}
.set {len_ch} // tap out to preserve length of CHUNKFASTA list
.set {len_ch} // tap out to preserve length of SEQKIT_SPLIT list

len_ch // tap swapped with set as tap stops pipeline completion
.map {meta, files ->
Expand Down Expand Up @@ -216,4 +216,3 @@ workflow SELFCOMP {
ch_bigbed = UCSC_BEDTOBIGBED.out.bigbed
versions = ch_versions.ifEmpty(null)
}

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