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 | ||
|
|
@@ -13,13 +14,17 @@ input: | |
| output: | ||
| - SAM/BAM/CRAM file. This must be the first output file in the output file list. | ||
| - idx: Optional path to bam index. | ||
| # - metrics: Optional path to metrics file. | ||
| # - unaligned: Optional path to unaligned unpaired reads. | ||
| # - unpaired: Optional path to unpaired reads that aligned at least once. | ||
| # - unconcordant: Optional path to pairs that didn't align concordantly. | ||
| # - concordant: Optional path to pairs that aligned concordantly at least once. | ||
| 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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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,4 +1,4 @@ | ||
| rule test_bowtie2_sam: | ||
| input: | ||
| sample=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], | ||
| idx=multiext( | ||
|
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@@ -10,25 +10,16 @@ rule test_bowtie2: | |
| ".rev.1.bt2", | ||
| ".rev.2.bt2", | ||
| ), | ||
| output: | ||
| "mapped_sam/{sample}.sam", | ||
| log: | ||
| "logs/bowtie2/mapped_sam_{sample}.log", | ||
| threads: 8 # Use at least two threads | ||
| wrapper: | ||
| "master/bio/bowtie2/align" | ||
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| use rule test_bowtie2_sam as test_bowtie2_se_gz with: | ||
| input: | ||
| sample=["reads/{sample}.1.fastq.gz"], | ||
| idx=multiext( | ||
|
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@@ -42,38 +33,26 @@ use rule test_bowtie2 as test_bowtie2_se_gz with: | |
| ), | ||
| output: | ||
| "mapped_se_gz/{sample}.bam", | ||
| log: | ||
| "logs/bowtie2/mapped_se_gz_{sample}.log", | ||
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| use rule test_bowtie2_sam as test_bowtie2_extra_outputs with: | ||
| output: | ||
| "mapped_multi/{sample}.bam", | ||
| idx="mapped_multi/{sample}.bam.bai", | ||
| # metrics="mapped_multi/{sample}.metrics.txt", | ||
| # unaligned=["mapped_multi/{sample}.unaligned.1.fq"], | ||
| # unpaired="mapped_multi/{sample}.unpaired.fq"], | ||
| # unconcordant="mapped_multi/{sample}.unconcordant.sam", | ||
| # concordant="mapped_multi/{sample}.concordant.sam", | ||
| log: | ||
| "logs/bowtie2/mapped_multi_{sample}.log", | ||
| params: | ||
| sort_program="samtools", | ||
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| use rule test_bowtie2_sam as test_bowtie2_cram with: | ||
| input: | ||
| sample=["reads/{sample}.1.fastq", "reads/{sample}.2.fastq"], | ||
| idx=multiext( | ||
|
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@@ -86,18 +65,26 @@ rule test_bowtie2_cram: | |
| ".rev.2.bt2", | ||
| ), | ||
| ref="genome.fasta", | ||
| ref_fai="genome.fasta.fai", | ||
| output: | ||
|
There was a problem hiding this comment. 🛠️ Refactor suggestion Make the reference index path configurable The hardcoded path - ref_fai="genome.fasta.fai",
+ ref_fai=config["ref_fai"], # or another configurable source
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| "mapped_cram/{sample}.cram", | ||
| log: | ||
| "logs/bowtie2/samtools_cram_{sample}.log", | ||
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| use rule test_bowtie2_sam as test_bowtie2_sort_samtools with: | ||
| output: | ||
| "mapped_samtools/{sample}.bam", | ||
| log: | ||
| "logs/bowtie2/mapped_samtools_{sample}.log", | ||
| params: | ||
| sort_program="samtools" | ||
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| use rule test_bowtie2_sam as test_bowtie2_sort_picard with: | ||
| output: | ||
| "mapped_picard/{sample}.bam", | ||
| log: | ||
| "logs/bowtie2/mapped_picard_{sample}.log", | ||
| params: | ||
| sort_program="picard" | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| Sheila 20 8 20 21 |
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