mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-21 15:56:03 +00:00
Subsitute samtools/bam2fq with samtools/fastq
This commit is contained in:
sofstam
parent
58795264e4
commit
102d53bd75
6 changed files with 250 additions and 53 deletions
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@ -21,7 +21,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
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- [Bowtie2](#bowtie2) - Host removal for Illumina reads
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- [minimap2](#minimap2) - Host removal for Nanopore reads
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- [SAMtools stats](#samtools-stats) - Statistics from host removal
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- [SAMtools bam2fq](#samtools-bam2fq) - Converts unmapped BAM file to fastq format (minimap2 only)
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- [SAMtools fastq](#samtools-fastq) - Converts unmapped BAM file to fastq format (minimap2 only)
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- [Bracken](#bracken) - Taxonomic classifier using k-mers and abundance estimations
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- [Kraken2](#kraken2) - Taxonomic classifier using exact k-mer matches
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- [KrakenUniq](#krakenuniq) - Taxonomic classifier that combines the k-mer-based classification and the number of unique k-mers found in each species
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@ -201,7 +201,7 @@ It is used with nf-core/taxprofiler to allow removal of 'host' (e.g. human) and/
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By default nf-core/taxprofiler will only provide the `.log` file if host removal is turned on. You will only have a `.bam` file if you specify `--save_hostremoval_bam`. This will contain _both_ mapped and unmapped reads. You will only get FASTQ files if you specify to save `--save_hostremoval_unmapped` - these contain only unmapped reads.
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> ℹ️ Unmapped reads in FASTQ are only found in this directory for short-reads, for long-reads see [`samtools/bam2fq/`](#samtools-bam2fq)
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> ℹ️ Unmapped reads in FASTQ are only found in this directory for short-reads, for long-reads see [`samtools/fastq/`](#samtools-fastq)
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> ⚠️ The resulting `.fastq` files may _not_ always be the 'final' reads that go into taxprofiling, if you also run other steps such as run merging etc..
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@ -228,11 +228,11 @@ By default, nf-core/taxprofiler will only provide the `.bam` file containing map
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> ℹ️ minimap2 is not yet supported as a module in MultiQC and therefore there is no dedicated section in the MultiQC HTML. Rather, alignment statistics to host genome is reported via samtools stats module in MultiQC report.
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> ℹ️ Unlike Bowtie2, minimap2 does not produce an unmapped FASTQ file by itself. See [`samtools/bam2fq`](#samtools-bam2fq)
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> ℹ️ Unlike Bowtie2, minimap2 does not produce an unmapped FASTQ file by itself. See [`samtools/fastq`](#samtools-fastq)
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### SAMtools bam2fq
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### SAMtools fastq
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[SAMtools bam2fq](http://www.htslib.org/doc/1.1/samtools.html) converts a `.sam`, `.bam`, or `.cram` alignment file to FASTQ format
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[SAMtools fastq](http://www.htslib.org/doc/1.1/samtools.html) converts a `.sam`, `.bam`, or `.cram` alignment file to FASTQ format
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<details markdown="1">
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<summary>Output files</summary>
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177
modules.json
177
modules.json
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@ -8,217 +8,308 @@
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"adapterremoval": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bbmap/bbduk": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bowtie2/align": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bowtie2/build": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bracken/bracken": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"bracken/combinebrackenoutputs": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"cat/fastq": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"centrifuge/centrifuge": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"centrifuge/kreport": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"custom/dumpsoftwareversions": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"diamond/blastx": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"falco": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"],
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/falco/falco.diff"
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},
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"fastp": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"fastqc": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"filtlong": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"gunzip": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"kaiju/kaiju": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"kaiju/kaiju2krona": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"kaiju/kaiju2table": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"kraken2/kraken2": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krakentools/combinekreports": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krakentools/kreport2krona": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krakenuniq/preloadedkrakenuniq": {
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"branch": "master",
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"git_sha": "a6eb17f65b3ee5761c25c075a6166c9f76733cee",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krona/ktimporttaxonomy": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"krona/ktimporttext": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"malt/run": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"megan/rma2info": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"metaphlan3/mergemetaphlantables": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"metaphlan3/metaphlan3": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"minimap2/align": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"minimap2/index": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"motus/merge": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"motus/profile": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"multiqc": {
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"branch": "master",
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"git_sha": "ee80d14721e76e2e079103b8dcd5d57129e584ba",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"porechop/porechop": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"],
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"installed_by": [
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"modules"
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],
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"patch": "modules/nf-core/porechop/porechop/porechop-porechop.diff"
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},
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"prinseqplusplus": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/bam2fq": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/fastq": {
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"branch": "master",
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"git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
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"installed_by": [
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"modules"
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]
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},
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"samtools/index": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/stats": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"samtools/view": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"taxpasta/merge": {
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"branch": "master",
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"git_sha": "ffa9641ee18f88aff974257cb50ba3cf8f7d143c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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},
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"untar": {
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"branch": "master",
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"git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
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"installed_by": ["modules"]
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"installed_by": [
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"modules"
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]
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}
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}
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}
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}
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}
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}
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}
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44
modules/nf-core/samtools/fastq/main.nf
generated
Normal file
44
modules/nf-core/samtools/fastq/main.nf
generated
Normal file
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@ -0,0 +1,44 @@
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process SAMTOOLS_FASTQ {
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tag "$meta.id"
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label 'process_low'
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conda "bioconda::samtools=1.16.1"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/samtools:1.16.1--h6899075_1' :
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'quay.io/biocontainers/samtools:1.16.1--h6899075_1' }"
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input:
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tuple val(meta), path(input)
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val(interleave)
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output:
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tuple val(meta), path("*_{1,2}.fastq.gz") , optional:true, emit: fastq
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tuple val(meta), path("*_interleaved.fastq.gz"), optional:true, emit: interleaved
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tuple val(meta), path("*_singleton.fastq.gz") , optional:true, emit: singleton
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tuple val(meta), path("*_other.fastq.gz") , optional:true, emit: other
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def output = ( interleave && ! meta.single_end ) ? "> ${prefix}_interleaved.fastq.gz" :
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meta.single_end ? "-1 ${prefix}_1.fastq.gz -s ${prefix}_singleton.fastq.gz" :
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"-1 ${prefix}_1.fastq.gz -2 ${prefix}_2.fastq.gz -s ${prefix}_singleton.fastq.gz"
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"""
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samtools \\
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fastq \\
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$args \\
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--threads ${task.cpus-1} \\
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-0 ${prefix}_other.fastq.gz \\
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$input \\
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$output
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
|
||||
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
|
||||
END_VERSIONS
|
||||
"""
|
||||
}
|
||||
62
modules/nf-core/samtools/fastq/meta.yml
generated
Normal file
62
modules/nf-core/samtools/fastq/meta.yml
generated
Normal file
|
|
@ -0,0 +1,62 @@
|
|||
name: samtools_fastq
|
||||
description: Converts a SAM/BAM/CRAM file to FASTQ
|
||||
keywords:
|
||||
- bam
|
||||
- sam
|
||||
- cram
|
||||
- fastq
|
||||
tools:
|
||||
- samtools:
|
||||
description: |
|
||||
SAMtools is a set of utilities for interacting with and post-processing
|
||||
short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li.
|
||||
These files are generated as output by short read aligners like BWA.
|
||||
homepage: http://www.htslib.org/
|
||||
documentation: http://www.htslib.org/doc/samtools.html
|
||||
doi: 10.1093/bioinformatics/btp352
|
||||
licence: ["MIT"]
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- input:
|
||||
type: file
|
||||
description: BAM/CRAM/SAM file
|
||||
pattern: "*.{bam,cram,sam}"
|
||||
- interleave:
|
||||
type: boolean
|
||||
description: Set true for interleaved fastq file
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software versions
|
||||
pattern: "versions.yml"
|
||||
- fastq:
|
||||
type: file
|
||||
description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files.
|
||||
pattern: "*_{1,2}.fastq.gz"
|
||||
- interleaved:
|
||||
type: file
|
||||
description: Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file.
|
||||
pattern: "*_interleaved.fastq.gz"
|
||||
- singleton:
|
||||
type: file
|
||||
description: Compressed FASTQ file with singleton reads
|
||||
pattern: "*_singleton.fastq.gz"
|
||||
- other:
|
||||
type: file
|
||||
description: Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset
|
||||
pattern: "*_other.fastq.gz"
|
||||
|
||||
authors:
|
||||
- "@priyanka-surana"
|
||||
- "@suzannejin"
|
||||
|
|
@ -304,7 +304,7 @@
|
|||
"type": "boolean",
|
||||
"fa_icon": "fas fa-save",
|
||||
"description": "Save reads from samples that went through the host-removal step",
|
||||
"help_text": "Save only the reads NOT mapped to the reference genome in FASTQ format (as exported from `samtools view` and `bam2fq`).\n\nThis can be useful if you wish to perform other analyses on the off-target reads from the host mapping, such as manual profiling or _de novo_ assembly."
|
||||
"help_text": "Save only the reads NOT mapped to the reference genome in FASTQ format (as exported from `samtools view` and `fastq`).\n\nThis can be useful if you wish to perform other analyses on the off-target reads from the host mapping, such as manual profiling or _de novo_ assembly."
|
||||
}
|
||||
},
|
||||
"fa_icon": "fas fa-user-times"
|
||||
|
|
|
|||
|
|
@ -5,7 +5,7 @@
|
|||
include { MINIMAP2_INDEX } from '../../modules/nf-core/minimap2/index/main'
|
||||
include { MINIMAP2_ALIGN } from '../../modules/nf-core/minimap2/align/main'
|
||||
include { SAMTOOLS_VIEW } from '../../modules/nf-core/samtools/view/main'
|
||||
include { SAMTOOLS_BAM2FQ } from '../../modules/nf-core/samtools/bam2fq/main'
|
||||
include { SAMTOOLS_FASTQ } from '../../modules/nf-core/samtools/fastq/main'
|
||||
include { SAMTOOLS_INDEX } from '../../modules/nf-core/samtools/index/main'
|
||||
include { SAMTOOLS_STATS } from '../../modules/nf-core/samtools/stats/main'
|
||||
|
||||
|
|
@ -38,8 +38,8 @@ workflow LONGREAD_HOSTREMOVAL {
|
|||
SAMTOOLS_VIEW ( ch_minimap2_mapped , [], [] )
|
||||
ch_versions = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
|
||||
|
||||
SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )
|
||||
ch_versions = ch_versions.mix( SAMTOOLS_BAM2FQ.out.versions.first() )
|
||||
SAMTOOLS_FASTQ ( SAMTOOLS_VIEW.out.bam, false )
|
||||
ch_versions = ch_versions.mix( SAMTOOLS_FASTQ.out.versions.first() )
|
||||
|
||||
// Indexing whole BAM for host removal statistics
|
||||
SAMTOOLS_INDEX ( MINIMAP2_ALIGN.out.bam )
|
||||
|
|
@ -54,7 +54,7 @@ workflow LONGREAD_HOSTREMOVAL {
|
|||
|
||||
emit:
|
||||
stats = SAMTOOLS_STATS.out.stats //channel: [val(meta), [reads ] ]
|
||||
reads = SAMTOOLS_BAM2FQ.out.reads // channel: [ val(meta), [ reads ] ]
|
||||
reads = SAMTOOLS_FASTQ.out.fastq // channel: [ val(meta), [ reads ] ]
|
||||
versions = ch_versions // channel: [ versions.yml ]
|
||||
mqc = ch_multiqc_files
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in a new issue