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Merged
lnblum merged 1 commit into from
Apr 20, 2026
Merged

add arabidopsis and t2t_chm13_v2+meth_controls+m13+phix #55

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10 changes: 10 additions & 0 deletions conf/references.config
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,16 @@ params {
genome_fa: "/mnt/galaxy/galaxyworks/tool-data/t2t_2.0_eschColi_K12_bs_controls/bwameth_index/t2t_2.0_eschColi_K12_bs_controls/t2t_2.0_eschColi_K12_bs_controls.fa",
genome_fai: "/mnt/galaxy/galaxyworks/tool-data/t2t_2.0_eschColi_K12_bs_controls/bwameth_index/t2t_2.0_eschColi_K12_bs_controls/t2t_2.0_eschColi_K12_bs_controls.fa.fai",
],
'arabidopsis_thaliana_TAIR12_bs_controls': [
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",
Comment on lines +20 to +27
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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).

Suggested change
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",

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Comment on lines +25 to +27
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Copilot AI Apr 20, 2026

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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).

Suggested change
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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],
'test': [
bwa_index: "${projectDir}/tests/fixtures/reference_files/reference.fa",
genome_fa: "${projectDir}/tests/fixtures/reference_files/reference.fa",
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