Description

Align reads to a reference genome using bowtie2 then sort with samtools

Input

Name (Type)
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 (directory)

STAR genome index

star

ch_gtf (file)

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

*.gtf

val_star_ignore_sjdbgtf (boolean)

If true the —sjdbGTFfile flag is set

true|false

val_seq_platform (string)

Sequencing platform to be added to the bam header using the —outSAMattrRGline flag

val_seq_center (string)

Sequencing center to be added to the bam header using the —outSAMattrRGline flag

ch_fasta (file)

Reference genome fasta file

*.{fasta,fa,fna}

ch_transcripts_fasta (file)

Optional reference genome fasta file

*.{fasta,fa,fna}

Output

Name (Type)
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) ]

orig_bam_transcript

Output BAM file of transcriptome alignment (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) ]

bam

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

bai

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

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) ]

bai_transcript

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

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) ]

versions (file)

File containing software versions

versions.yml
included in
riboseq rnadnavar
included modules and subworkflows
star/align samtools/sort samtools/index samtools/stats samtools/idxstats samtools/flagstat bam_sort_stats_samtools
maintainer
Github user JoseEspinosa
get in touch
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