Upgraded packages
| Package | v_1.0.0 | v_1.1.0 | v_1.1.1 | v_1.2.0 |
|---|---|---|---|---|
| bwa | 0.7.17 | 0.7.18 | 0.7.19 | -- |
| samtools | 1.19 | 1.20 | 1.21 | 1.23.1 |
| picard | 2.18.7 | 3.2.0 | 3.4.0 | -- |
| bandage | 0.8.1 | -- | 0.9.0 | -- |
| busco | 5.7.0 | 5.7.1 | 5.8.3 | 6.0.0 |
| fastp | 0.23.4 | -- | 0.24.1 | 1.3.1 |
| fcsgx | 0.5.0 | 0.5.4 | 0.5.5 | -- |
| gfastats | 1.3.6 | -- | 1.3.11 | -- |
| hifiasm | 0.19.8 | 0.19.9 | 0.25.0 | -- |
| nanoplot | 1.42.0 | 1.43.0 | 1.44.1 | 1.46.2 |
| quast | 5.2.0 | -- | 5.3.0 | -- |
| yahs | 1.2a.2 | -- | 1.2.2 | -- |
The bwa mem commands in workflow/rules/bwa_mem.smk was modified from:
(bwa mem -M -t {threads} {input.REF} {input.forward_hic} | samtools view -@ {threads} -Sb - > {output.bam1}) >> {log} 2>&1
(bwa mem -M -t {threads} {input.REF} {input.reverse_hic} | samtools view -@ {threads} -Sb - > {output.bam2}) >> {log} 2>&1
to:
(bwa mem -5SPM -t {threads} {input.REF} {input.forward_hic} | samtools view -@ {threads} -Sb - > {output.bam1}) >> {log} 2>&1
(bwa mem -5SPM -t {threads} {input.REF} {input.reverse_hic} | samtools view -@ {threads} -Sb - > {output.bam2}) >> {log} 2>&1