validation aligner binds in scripts at read time

LANL-Bioinformatics · Jan 22, 2025 · 7516637 · 7516637
1 parent ce738ed
commit 7516637
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Showing 8 changed files with 1 addition and 8 deletions.
diff --git a/workflows/Nextflow/modules/runReadsToContig/Dockerfile b/workflows/Nextflow/modules/runReadsToContig/Dockerfile
@@ -23,13 +23,6 @@ RUN conda install -n readsToContig -c bioconda samtools=1.6
 RUN conda install -c conda-forge conda-pack
 
 
-ADD bin/bam_to_fastq.pl /opt/conda/envs/readsToContig/bin
-ADD bin/contig_stats.pl /opt/conda/envs/readsToContig/bin
-ADD bin/ContigCoverageFold_plots_from_samPileup.pl /opt/conda/envs/readsToContig/bin
-ADD bin/fastq_utility.pm /opt/conda/envs/readsToContig/bin
-ADD bin/runReadsToContig.pl /opt/conda/envs/readsToContig/bin
-ADD bin/tab2Json_for_dataTable.pl /opt/conda/envs/readsToContig/bin
-
 RUN conda-pack -n readsToContig -o /tmp/env.tar && \
     mkdir /venv && cd /venv && tar xf /tmp/env.tar && \
     rm /tmp/env.tar

diff --git a/...ontigCoverageFold_plots_from_samPileup.pl → ...ontigCoverageFold_plots_from_samPileup.pl b/...ontigCoverageFold_plots_from_samPileup.pl → ...ontigCoverageFold_plots_from_samPileup.pl
diff --git a/...ules/runReadsToContig/bin/bam_to_fastq.pl → ...oContig/resources/usr/bin/bam_to_fastq.pl b/...ules/runReadsToContig/bin/bam_to_fastq.pl → ...oContig/resources/usr/bin/bam_to_fastq.pl
diff --git a/...ules/runReadsToContig/bin/contig_stats.pl → ...oContig/resources/usr/bin/contig_stats.pl b/...ules/runReadsToContig/bin/contig_stats.pl → ...oContig/resources/usr/bin/contig_stats.pl
diff --git a/...les/runReadsToContig/bin/fastq_utility.pm → ...Contig/resources/usr/bin/fastq_utility.pm b/...les/runReadsToContig/bin/fastq_utility.pm → ...Contig/resources/usr/bin/fastq_utility.pm
diff --git a/.../runReadsToContig/bin/runReadsToContig.pl → ...tig/resources/usr/bin/runReadsToContig.pl b/.../runReadsToContig/bin/runReadsToContig.pl → ...tig/resources/usr/bin/runReadsToContig.pl
diff --git a/...adsToContig/bin/tab2Json_for_dataTable.pl → ...sources/usr/bin/tab2Json_for_dataTable.pl b/...adsToContig/bin/tab2Json_for_dataTable.pl → ...sources/usr/bin/tab2Json_for_dataTable.pl
diff --git a/workflows/Nextflow/nextflow.config b/workflows/Nextflow/nextflow.config
@@ -160,7 +160,7 @@ process {
         container = 'apwat/run_assembly:1.5'
     }
     withLabel: 'r2c' {
-        container = 'apwat/run_r2c:1.6'
+        container = 'apwat/run_r2c:1.7'
     }
     withLabel: 'rta' {
         container = 'apwat/reads_taxonomy:1.14'