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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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8 changes: 6 additions & 2 deletions bio/bowtie2/align/environment.linux-64.pin.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.13-hb9d3cd8_0.conda
https://conda.anaconda.org/conda-forge/linux-64/c-ares-1.34.3-hb9d3cd8_1.conda#ee228789a85f961d14567252a03e725f
https://conda.anaconda.org/conda-forge/linux-64/libexpat-2.6.4-h5888daf_0.conda#db833e03127376d461e1e13e76f09b6c
https://conda.anaconda.org/conda-forge/linux-64/libgcc-ng-14.2.0-h69a702a_1.conda#e39480b9ca41323497b05492a63bc35b
https://conda.anaconda.org/conda-forge/linux-64/liblzma-5.6.3-hb9d3cd8_1.conda#2ecf2f1c7e4e21fcfe6423a51a992d84
https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-14.2.0-hc0a3c3a_1.conda#234a5554c53625688d51062645337328
https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.1-hb9d3cd8_2.conda#edb0dca6bc32e4f4789199455a1dbeb8
https://conda.anaconda.org/conda-forge/linux-64/openssl-3.4.0-hb9d3cd8_0.conda#23cc74f77eb99315c0360ec3533147a9
Expand All @@ -37,6 +38,7 @@ https://conda.anaconda.org/conda-forge/linux-64/libev-4.33-hd590300_2.conda#172b
https://conda.anaconda.org/conda-forge/linux-64/libffi-3.4.2-h7f98852_5.tar.bz2#d645c6d2ac96843a2bfaccd2d62b3ac3
https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-hd590300_2.conda#d66573916ffcf376178462f1b61c941e
https://conda.anaconda.org/conda-forge/linux-64/libjpeg-turbo-3.0.0-hd590300_1.conda#ea25936bb4080d843790b586850f82b8
https://conda.anaconda.org/conda-forge/linux-64/liblzma-devel-5.6.3-hb9d3cd8_1.conda#cc4687e1814ed459f3bd6d8e05251ab2
https://conda.anaconda.org/conda-forge/linux-64/libmpdec-4.0.0-h4bc722e_0.conda#aeb98fdeb2e8f25d43ef71fbacbeec80
https://conda.anaconda.org/conda-forge/linux-64/libpng-1.6.44-hadc24fc_0.conda#f4cc49d7aa68316213e4b12be35308d1
https://conda.anaconda.org/conda-forge/linux-64/libsqlite-3.47.0-hadc24fc_1.conda#b6f02b52a174e612e89548f4663ce56a
Expand All @@ -48,7 +50,8 @@ https://conda.anaconda.org/conda-forge/linux-64/libxcb-1.17.0-h8a09558_0.conda#9
https://conda.anaconda.org/conda-forge/linux-64/libxcrypt-4.4.36-hd590300_1.conda#5aa797f8787fe7a17d1b0821485b5adc
https://conda.anaconda.org/conda-forge/linux-64/ncurses-6.5-he02047a_1.conda#70caf8bb6cf39a0b6b7efc885f51c0fe
https://conda.anaconda.org/conda-forge/linux-64/tk-8.6.13-noxft_h4845f30_101.conda#d453b98d9c83e71da0741bb0ff4d76bc
https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2#2161070d867d1b1204ea749c8eec4ef0
https://conda.anaconda.org/conda-forge/linux-64/xz-gpl-tools-5.6.3-hbcc6ac9_1.conda#f529917bab7862aaad6867bf2ea47a99
https://conda.anaconda.org/conda-forge/linux-64/xz-tools-5.6.3-hb9d3cd8_1.conda#de3f31a6eed01bc2b8c7dcad07ad9034
https://conda.anaconda.org/conda-forge/linux-64/zlib-1.3.1-hb9d3cd8_2.conda#c9f075ab2f33b3bbee9e62d4ad0a6cd8
https://conda.anaconda.org/conda-forge/linux-64/freetype-2.12.1-h267a509_2.conda#9ae35c3d96db2c94ce0cef86efdfa2cb
https://conda.anaconda.org/conda-forge/linux-64/graphite2-1.3.13-h59595ed_1003.conda#f87c7b7c2cb45f323ffbce941c78ab7c
Expand All @@ -61,7 +64,8 @@ https://conda.anaconda.org/conda-forge/linux-64/perl-5.32.1-7_hd590300_perl5.con
https://conda.anaconda.org/conda-forge/linux-64/pixman-0.43.2-h59595ed_0.conda#71004cbf7924e19c02746ccde9fd7123
https://conda.anaconda.org/conda-forge/linux-64/readline-8.2-h8228510_1.conda#47d31b792659ce70f470b5c82fdfb7a4
https://conda.anaconda.org/conda-forge/linux-64/xorg-libsm-1.2.4-he73a12e_1.conda#05a8ea5f446de33006171a7afe6ae857
https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.10-h4f16b4b_0.conda#0b666058a179b744a622d0a4a0c56353
https://conda.anaconda.org/conda-forge/linux-64/xorg-libx11-1.8.10-h4f16b4b_1.conda#125f34a17d7b4bea418a83904ea82ea6
https://conda.anaconda.org/conda-forge/linux-64/xz-5.6.3-hbcc6ac9_1.conda#62aae173382a8aae284726353c6a6a24
https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda#4d056880988120e29d75bfff282e0f45
https://conda.anaconda.org/conda-forge/linux-64/fontconfig-2.15.0-h7e30c49_1.conda#8f5b0b297b59e1ac160ad4beec99dbee
https://conda.anaconda.org/conda-forge/linux-64/krb5-1.21.3-h659f571_0.conda#3f43953b7d3fb3aaa1d0d0723d91e368
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6 changes: 3 additions & 3 deletions bio/bowtie2/align/environment.yaml
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Expand Up @@ -3,7 +3,7 @@ channels:
- bioconda
- nodefaults
dependencies:
- bowtie2 =2.5.4
- picard-slim =3.3.0
- bowtie2 =2.5
- 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
1 change: 1 addition & 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
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2 changes: 1 addition & 1 deletion bio/bowtie2/align/wrapper.py
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@@ -1,4 +1,4 @@
__author__ = "Johannes Köster"
__author__ = "Johannes Köster, Jorge Langa"
__copyright__ = "Copyright 2016, Johannes Köster"
__email__ = "[email protected]"
__license__ = "MIT"
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