add arabidopsis and t2t_chm13_v2+meth_controls+m13+phix#55
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Pull request overview
Adds new reference-genome entries to the pipeline’s conf/references.config so users can select additional genomes via --genome.
Changes:
- Added
arabidopsis_thaliana_TAIR12_bs_controlsreference paths (FA/FAI + bwa-meth reference). - Added
t2t_chm13_v2+meth_controls+m13+phixreference paths (FA/FAI + bwa-meth reference).
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| bwa_index: "/bioinfo/ref/arabidopsis_thaliana_TAIR12_bs_controls/bwameth/arabidopsis_thaliana_TAIR12_bs_controls.fa", | ||
| genome_fa: "/bioinfo/ref/arabidopsis_thaliana_TAIR12_bs_controls/bwameth/arabidopsis_thaliana_TAIR12_bs_controls.fa", | ||
| genome_fai: "/bioinfo/ref/arabidopsis_thaliana_TAIR12_bs_controls/bwameth/arabidopsis_thaliana_TAIR12_bs_controls.fa.fai", | ||
| ], | ||
| 't2t_chm13_v2+meth_controls+m13+phix': [ | ||
| bwa_index: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa", | ||
| genome_fa: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa", | ||
| genome_fai: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa.fai", |
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These new reference paths use a /bwameth/ directory, while the existing entries (and README.md guidance) use /bwameth_index/ to indicate the location where bwa-meth/BWA index files exist. If the index files are actually under a bwameth_index directory (as with the other genomes), this will cause alignment to fail when --genome arabidopsis_thaliana_TAIR12_bs_controls is selected. Please align the directory structure/path with the established bwameth_index/.../<genome>.fa convention (or update to the correct index location if /bwameth/ is intentional and contains the required index files).
| bwa_index: "/bioinfo/ref/arabidopsis_thaliana_TAIR12_bs_controls/bwameth/arabidopsis_thaliana_TAIR12_bs_controls.fa", | |
| genome_fa: "/bioinfo/ref/arabidopsis_thaliana_TAIR12_bs_controls/bwameth/arabidopsis_thaliana_TAIR12_bs_controls.fa", | |
| genome_fai: "/bioinfo/ref/arabidopsis_thaliana_TAIR12_bs_controls/bwameth/arabidopsis_thaliana_TAIR12_bs_controls.fa.fai", | |
| ], | |
| 't2t_chm13_v2+meth_controls+m13+phix': [ | |
| bwa_index: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa", | |
| genome_fa: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa", | |
| genome_fai: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa.fai", | |
| bwa_index: "/bioinfo/ref/arabidopsis_thaliana_TAIR12_bs_controls/bwameth_index/arabidopsis_thaliana_TAIR12_bs_controls/arabidopsis_thaliana_TAIR12_bs_controls.fa", | |
| genome_fa: "/bioinfo/ref/arabidopsis_thaliana_TAIR12_bs_controls/bwameth_index/arabidopsis_thaliana_TAIR12_bs_controls/arabidopsis_thaliana_TAIR12_bs_controls.fa", | |
| genome_fai: "/bioinfo/ref/arabidopsis_thaliana_TAIR12_bs_controls/bwameth_index/arabidopsis_thaliana_TAIR12_bs_controls/arabidopsis_thaliana_TAIR12_bs_controls.fa.fai", | |
| ], | |
| 't2t_chm13_v2+meth_controls+m13+phix': [ | |
| bwa_index: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth_index/t2t_chm13_v2+meth_controls+m13+phix/t2t_chm13_v2+meth_controls+m13+phix.fa", | |
| genome_fa: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth_index/t2t_chm13_v2+meth_controls+m13+phix/t2t_chm13_v2+meth_controls+m13+phix.fa", | |
| genome_fai: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth_index/t2t_chm13_v2+meth_controls+m13+phix/t2t_chm13_v2+meth_controls+m13+phix.fa.fai", |
| bwa_index: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa", | ||
| genome_fa: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa", | ||
| genome_fai: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa.fai", |
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Same issue as above: this entry points to /bwameth/.../*.fa instead of following the existing /bwameth_index/<genome>/<genome>.fa pattern used elsewhere in this config and described in README.md. If the bwameth/BWA indices are not colocated with this fasta, bwameth.py --reference will error at runtime. Please ensure this path points at the fasta in the directory that contains the prebuilt indices (or rename/move to match the bwameth_index layout).
| bwa_index: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa", | |
| genome_fa: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa", | |
| genome_fai: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth/t2t_chm13_v2+meth_controls+m13+phix.fa.fai", | |
| bwa_index: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth_index/t2t_chm13_v2+meth_controls+m13+phix/t2t_chm13_v2+meth_controls+m13+phix.fa", | |
| genome_fa: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth_index/t2t_chm13_v2+meth_controls+m13+phix/t2t_chm13_v2+meth_controls+m13+phix.fa", | |
| genome_fai: "/bioinfo/ref/t2t_chm13_v2+meth_controls+m13+phix/bwameth_index/t2t_chm13_v2+meth_controls+m13+phix/t2t_chm13_v2+meth_controls+m13+phix.fa.fai", |
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