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feat: bowtie2 can now sort with samtools and picard #3518

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feat: bowtie2 can now sort with samtools and picard #3518

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6804755
feat: bowtie2 can now sort with samtools and picard
jlanga Dec 3, 2024
80998d3
fix: black wrapper
jlanga Dec 3, 2024
c653f32
fix: snakefmt and lint
jlanga Dec 3, 2024
9d58e61
fix: sort environment
jlanga Dec 3, 2024
b83e343
fix: remove duplicated params
jlanga Dec 3, 2024
e116b10
fix: it is sort_program
jlanga Dec 3, 2024
d48cf0f
fix: remove note on sort_program
jlanga Dec 3, 2024
be1b1ec
chore: add name
jlanga Dec 5, 2024
c784d94
chore: add name
jlanga Dec 5, 2024
734b1bb
fix: remove patch from version numbers
jlanga Dec 5, 2024
eac0db4
fix: Update bio/bowtie2/align/wrapper.py
jlanga Dec 5, 2024
d2646f4
refactor: rearrange everything, make pylint yell less
jlanga Dec 6, 2024
9c9c918
chore: merge conflict
jlanga Dec 6, 2024
c4f9cf3
fix: add fai file
jlanga Dec 6, 2024
badae1c
fix: typo in ref_fai
jlanga Dec 6, 2024
36b6145
chore: black
jlanga Dec 6, 2024
d97f32a
chore: remove unused stuff
jlanga Dec 6, 2024
ceba80f
fix: i'd swear that I had put the fai files before
jlanga Dec 6, 2024
ecdab94
chore: typo
jlanga Dec 6, 2024
a6b511a
refactor: uppercase constants and rearrange
jlanga Dec 12, 2024
056cd06
refactor: distinguish original variables from the ones generated for …
jlanga Dec 19, 2024
fb07443
refactor: rearrange everything, make the index creation work
jlanga Dec 19, 2024
2ed25a1
refactor: expand tests, comment extra output parts
jlanga Dec 19, 2024
c093576
refactor: spacing
jlanga Dec 19, 2024
dff2d94
chore: remove useless comment
jlanga Dec 19, 2024
eb499d4
feat: extend output checks
jlanga Dec 19, 2024
739c0eb
chore: remove f-string that are constant
jlanga Dec 19, 2024
0d03448
feat: extend threads checks
jlanga Dec 19, 2024
a2e6504
refactor: coderabbit suggestions
jlanga Dec 19, 2024
3bdc418
refactor: consolidate checks
jlanga Dec 19, 2024
b661b16
Merge branch 'master' into bowtie2_sort
jlanga Dec 20, 2024
949cfde
fix: fix picard-slim and re-pin everything
jlanga Dec 20, 2024
a2dc334
Merge branch 'bowtie2_sort' of github.com:jlanga/snakemake-wrappers i…
jlanga Dec 20, 2024
8242918
fix: pin everything but samtools
jlanga Dec 20, 2024
a93881a
fix: --with-header
jlanga Dec 20, 2024
7ba5b46
fix: use coderrabit suggestions
jlanga Dec 20, 2024
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93 changes: 70 additions & 23 deletions bio/bowtie2/align/environment.linux-64.pin.txt
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Original file line number Diff line number Diff line change
@@ -1,46 +1,93 @@
# 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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https://conda.anaconda.org/conda-forge/linux-64/xorg-libxtst-1.2.5-hb9d3cd8_3.conda#7bbe9a0cc0df0ac5f5a8ad6d6a11af2f
https://conda.anaconda.org/conda-forge/linux-64/openjdk-23.0.1-h4c11d01_0.conda#c40dda22ec391102c2bc24dd92f1f663
https://conda.anaconda.org/bioconda/linux-64/samtools-1.21-h50ea8bc_0.tar.bz2#4a7fe11223f61cb2d950ed54e20c12ce
https://conda.anaconda.org/bioconda/noarch/picard-slim-3.3.0-hdfd78af_0.tar.bz2#fab4a4639fd22cd155b740fce3064944
5 changes: 3 additions & 2 deletions bio/bowtie2/align/environment.yaml
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Expand Up @@ -3,6 +3,7 @@ channels:
- bioconda
- nodefaults
dependencies:
- bowtie2 =2.5.4
- bowtie2 =2.5
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- picard-slim =3.3
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Suggested change
- picard-slim =3.3
- picard-slim =3.3.0

- samtools =1.21
- snakemake-wrapper-utils =0.6.2
- snakemake-wrapper-utils =0.6
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5 changes: 5 additions & 0 deletions bio/bowtie2/align/meta.yaml
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Expand Up @@ -5,6 +5,7 @@ authors:
- Johannes Köster
- Filipe G. Vieira
- Thibault Dayris
- Jorge Langa
input:
- sample: FASTQ file(s)
- idx: Bowtie2 indexed reference index
Expand All @@ -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.
39 changes: 39 additions & 0 deletions bio/bowtie2/align/test/Snakefile
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Expand Up @@ -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}",
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💡 Codebase verification

Based on the analysis of both wrapper.py and the test Snakefile, I can now provide the final response:

CRAM output handling needs improvement

The wrapper doesn't explicitly validate the presence of the reference genome for CRAM output. While the test Snakefile correctly includes ref="genome.fasta" in CRAM-related rules, the wrapper.py should:

  • Validate reference presence when output is CRAM format
  • Properly pass the reference to samtools for CRAM generation

Specific issues:

  • In wrapper.py, line 54-55: The CRAM conversion lacks -T reference parameter in the samtools view command
  • No validation check for reference input when CRAM output is detected
🔗 Analysis chain

Verify CRAM output handling

The reference genome is required for CRAM output. Ensure proper error handling when ref is missing.

🏁 Scripts executed

The following scripts were executed for the analysis:

Script:

#!/bin/bash
# Description: Check if wrapper.py handles missing reference for CRAM output

# Search for CRAM-related error handling
rg -A 5 "\.cram" bio/bowtie2/align/wrapper.py

Length of output: 47

Script:

#!/bin/bash
# Let's check the wrapper.py content to understand how output formats are handled
cat bio/bowtie2/align/wrapper.py

Length of output: 5582

Script:

#!/bin/bash
# Let's check if there's any reference handling for CRAM output in the Snakefile
cat bio/bowtie2/align/test/Snakefile

Length of output: 4074

# 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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