fastq_align_star

Align reads to a reference genome using STAR then sort with samtools

alignfastagenomereference

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/fastq_align_star

Description

Align reads to a reference genome using STAR then sort with samtools

Input

name

description

pattern

`ch_reads`

List of input FastQ files of size 1 and 2 for single-end and paired-end data,
respectively.
Structure: [ val(meta), [ path(reads) ] ]

`ch_index`

STAR genome index

star

`ch_gtf`

GTF file used to set the splice junctions with the –sjdbGTFfile flag

*.gtf

`val_star_ignore_sjdbgtf`

If true the –sjdbGTFfile flag is set

true|false

`ch_fasta_fai`

Reference genome fasta file and index

*.{fasta,fa,fna,fai}

`ch_transcripts_fasta_fai`

Optional reference genome fasta file and index

*.{fasta,fa,fna,fai}

Output

name

description

pattern

`orig_bam`

Output BAM file containing read alignments
Structure: [ val(meta), path(bam) ]

`log_final`

STAR final log file
Structure: [ val(meta), path(log_final) ]

`log_out`

STAR log out file
Structure: [ val(meta), path(log_out) ]

`log_progress`

STAR log progress file
Structure: [ val(meta), path(log_progress) ]

`bam_sorted`

Sorted BAM file of read alignments (optional)
Structure: [ val(meta), path(bam) ]

`fastq`

Unmapped FastQ files (optional)
Structure: [ val(meta), path(fastq) ]

`tab`

STAR output tab file(s) (optional)
Structure: [ val(meta), path(tab) ]

`orig_bam_transcript`

Output BAM file of transcriptome alignment (optional)
Structure: [ val(meta), path(bam) ]

`bam`

BAM file ordered by samtools
Structure: [ val(meta), path(bam) ]

`index`

Index of the ordered BAM file
Structure: [ val(meta), path(index) ]

`stats`

File containing samtools stats output
Structure: [ val(meta), path(stats) ]

`flagstat`

File containing samtools flagstat output
Structure: [ val(meta), path(flagstat) ]

`idxstats`

File containing samtools idxstats output
Structure: [ val(meta), path(idxstats) ]

`bam_transcript`

Transcriptome-level BAM file ordered by samtools (optional)
Structure: [ val(meta), path(bam) ]

`index_transcript`

Transcriptome-level index of the ordered BAM file (optional)
Structure: [ val(meta), path(index) ]

`stats_transcript`

Transcriptome-level file containing samtools stats output (optional)
Structure: [ val(meta), path(stats) ]

`flagstat_transcript`

Transcriptome-level file containing samtools flagstat output (optional)
Structure: [ val(meta), path(flagstat) ]

`idxstats_transcript`

Transcriptome-level file containing samtools idxstats output (optional)
Structure: [ val(meta), path(idxstats) ]