feat: bowtie2 can now sort with samtools and picard #3518
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| # This file may be used to create an environment using: | ||
| # $ conda create --name <env> --file <this file> | ||
| # platform: linux-64 | ||
| # created-by: conda 24.9.2 | ||
| @EXPLICIT | ||
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@@ -5,6 +5,7 @@ authors: | |
| - Johannes Köster | ||
| - Filipe G. Vieira | ||
| - Thibault Dayris | ||
| - Jorge Langa | ||
| input: | ||
| - sample: FASTQ file(s) | ||
| - idx: Bowtie2 indexed reference index | ||
|
|
@@ -21,5 +22,9 @@ output: | |
| params: | ||
| - extra: additional program arguments (except for `-x`, `-U`, `-1`, `-2`, `--interleaved`, `-b`, `--met-file`, `--un`, `--al`, `--un-conc`, `--al-conc`, `-f`, `--tab6`, `--tab5`, `-q`, or `-p/--threads`) | ||
| - interleaved: Input `sample` contains interleaved paired-end FASTQ/FASTA reads. `False`(default) or `True`. | ||
| - sort_program: program to sort the output. `none`(default), `samtools`, or `picard`. | ||
| - sort_extra: additional arguments for samtools or picard when sorting. | ||
| - sort_order: choose between `coordinate`(default) or `queryname`. | ||
| notes: | | ||
| * The `extra` param allows for additional arguments for bowtie2. | ||
| * This wrapper uses an inner pipe. Make sure to use at least two threads in your Snakefile. | ||
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@@ -101,3 +101,42 @@ rule test_bowtie2_cram: | |
| threads: 8 # Use at least two threads | ||
| wrapper: | ||
| "master/bio/bowtie2/align" | ||
|
|
||
|
|
||
| for order in ["coordinate", "queryname"]: | ||
| for extension in ["sam", "bam", "cram"]: | ||
| for program in ["none", "samtools", "picard"]: | ||
|
|
||
| rule: | ||
| name: | ||
| f"bowtie2_align_{program}_{order}_{extension}" | ||
| input: | ||
| sample=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], | ||
| idx=multiext( | ||
| "index/genome", | ||
| ".1.bt2", | ||
| ".2.bt2", | ||
| ".3.bt2", | ||
| ".4.bt2", | ||
| ".rev.1.bt2", | ||
| ".rev.2.bt2", | ||
| ), | ||
| ref="genome.fasta", | ||
| output: | ||
| f"mapped_idx/{{sample}}.{program}_{order}.{extension}", | ||
|
||
| # idx="", | ||
| # metrics="", | ||
| # unaligned="", | ||
| # unpaired="", | ||
| # unconcordant="", | ||
| # concordant="", | ||
| params: | ||
| sort_program=program, | ||
| sort_order=order, | ||
| sort_extra="", | ||
| extra="", # optional parameters | ||
| log: | ||
| f"logs/bowtie2/{{sample}}.{program}_{order}_{extension}.log", | ||
| threads: 8 # Use at least two threads | ||
| wrapper: | ||
| "master/bio/bowtie2/align" | ||
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