Fix mtGrasp call in sub_then_run_mtgrasp.sh (#32)

* Fix mtGrasp call in sub_then_run_mtgrasp.sh * Pin python version in CI
bcgsc · Oct 16, 2024 · 2f4384e · 2f4384e
1 parent 1a29d35
commit 2f4384e
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Showing 2 changed files with 4 additions and 4 deletions.
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -20,7 +20,7 @@ jobs:
   - script: |
       source activate mtgrasp_ci
       conda install --yes -c bioconda -c conda-forge python mamba
-      mamba install --yes -c conda-forge -c bioconda snakemake 'blast>=2.9.0' biopython seqtk abyss ntjoin bwa samtools pilon ntcard 'mitos>=2.1.7'
+      mamba install --yes -c conda-forge -c bioconda snakemake 'blast>=2.9.0' biopython seqtk abyss ntjoin bwa samtools pilon ntcard 'mitos>=2.1.7' python=3.12
     displayName: Install dependencies
 
   - script: |
@@ -55,7 +55,7 @@ jobs:
 
   - script: |
       source activate mtgrasp_ci
-      mamba install --yes -c conda-forge -c bioconda snakemake 'blast>=2.9.0' biopython seqtk abyss ntjoin bwa samtools pilon ntcard 'mitos>=2.1.7'
+      mamba install --yes -c conda-forge -c bioconda snakemake 'blast>=2.9.0' biopython seqtk abyss ntjoin bwa samtools pilon ntcard 'mitos>=2.1.7' python=3.12
     displayName: Install dependencies
 
   - script: |

diff --git a/sub_then_run_mtgrasp.sh b/sub_then_run_mtgrasp.sh
@@ -41,6 +41,6 @@ else
     seqtk sample -s100 ${r2} ${subsample} | gzip > ${out_dir}/subsets/${read2_base}_${subsample}.fastq.gz &
     wait
 fi && snakemake -s ${script_dir}/mtgrasp.smk --cores ${threads} -p -k \
---config r1=${current_dir}${out_dir}/subsets/${read1_base}_${subsample}.fastq.gz r2=${current_dir}${out_dir}/subsets/${read2_base}_${subsample}.fastq.gz out_dir=${out_dir} mt_code=${mt_gen} k=${kmer} kc=${kc} ref_path=${ref_path} threads=${threads} \
-abyss_fpr=${abyss_fpr} sealer_fpr=${sealer_fpr} p=${p} sealer_k=${sealer_k} end_recov_sealer_fpr=${end_recov_sealer_fpr} \
+--config r1=${current_dir}${out_dir}/subsets/${read1_base}_${subsample}.fastq.gz r2=${current_dir}${out_dir}/subsets/${read2_base}_${subsample}.fastq.gz out_dir=${out_dir} mt_code=${mt_gen} kmer=${kmer} kc=${kc} ref_path=${ref_path} threads=${threads} \
+abyss_fpr=${abyss_fpr} sealer_fpr=${sealer_fpr} p_gapfill=${p} sealer_k=${sealer_k} end_recov_sealer_fpr=${end_recov_sealer_fpr} \
 end_recov_p=${end_recov_p} end_recov_sealer_k=${end_recov_sealer_k} mismatch_allowed=${mismatch_allowed} annotate=${annotate} mitos_path=${mitos_path} && rm ${out_dir}/subsets/*${subsample}.fastq.gz