Add python3 to the container

NBISweden · Nov 11, 2024 · aa67e98 · aa67e98
1 parent 924825b
commit aa67e98
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Showing 7 changed files with 35 additions and 35 deletions.
diff --git a/workflow/rules/0.1_reference_genome_preps.smk b/workflow/rules/0.1_reference_genome_preps.smk
@@ -48,7 +48,7 @@ rule samtools_fasta_index:
     group:
         "reference_prep_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools faidx {input.ref} 2> {log}

diff --git a/workflow/rules/1.2_map_to_mitogenomes.smk b/workflow/rules/1.2_map_to_mitogenomes.smk
@@ -185,7 +185,7 @@ rule map_historical_merged_to_mito:
     log:
         "results/logs/1.2_map_to_mitogenomes/{sample}_{index}_{lane}_{mitoref}_map_historical_merged_to_mito.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         bwa aln -l 16500 -n 0.01 -o 2 -t {threads} {input.ref} {input.merged} | \
@@ -208,7 +208,7 @@ rule map_historical_unmerged_to_mito:
     log:
         "results/logs/1.2_map_to_mitogenomes/{sample}_{index}_{lane}_{mitoref}_map_historical_unmerged_to_mito.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         bwa aln -l 16500 -n 0.01 -o 2 -t {threads} {input.ref} {input.R1_un} > {output.R1_sai} 2> {log} &&
@@ -228,7 +228,7 @@ rule mitogenome_bam_stats:
     log:
         "results/logs/1.2_map_to_mitogenomes/{sample}_{index}_{lane}_{reads}_{mitoref}_mitogenome_bam_stats.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -320,7 +320,7 @@ rule merge_historical_mitogenome_bams_per_sample:
     log:
         "results/logs/1.2_map_to_mitogenomes/{sample}_{mitoref}_merge_historical_mitogenome_bams_per_sample.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -345,7 +345,7 @@ rule merged_mitogenome_bam_stats:
     group:
         "historical_merged_mito_bams_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}

diff --git a/workflow/rules/13_GERP.smk b/workflow/rules/13_GERP.smk
@@ -331,7 +331,7 @@ rule align2target:
     log:
         "results/logs/13_GERP/alignment/" + REF_NAME + "/{gerpref}_align2target.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         bwa mem {params.extra} -t {threads} {input.target} {input.fastq} | \
@@ -349,7 +349,7 @@ rule index_gerp_bams:
     log:
         "results/logs/13_GERP/alignment/" + REF_NAME + "/{gerpref}_index_gerp_bams.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -366,7 +366,7 @@ rule gerp_bam_stats:
     log:
         "results/logs/13_GERP/alignment/" + REF_NAME + "/{gerpref}_gerp_bam_stats.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -411,7 +411,7 @@ rule bam2fasta:
         "results/logs/13_GERP/{chr}_chunks/" + REF_NAME + "/fasta/{gerpref}_{chunk}_bam2fasta.log",
     threads: 2
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"  # This container includes python 3.7.6 with default python modules
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"  # This container includes python 3.7.6 with default python modules
     shell:
         """
         if [ ! -d {output.fasta_dir} ]; then

diff --git a/workflow/rules/2_mapping.smk b/workflow/rules/2_mapping.smk
@@ -63,7 +63,7 @@ rule sai2bam:
         "results/logs/2_mapping/historical/" + REF_NAME + "/{sample}_{index}_{lane}_sai2bam.log",
     threads: 8
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         bwa samse -r $(cat {input.rg}) {input.ref} {input.sai} {input.fastq_hist} | \
@@ -104,7 +104,7 @@ rule map_modern:
         "results/logs/2_mapping/modern/" + REF_NAME + "/{sample}_{index}_{lane}_map_modern.log",
     threads: 8
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         bwa mem -M -t {threads} -R $(cat {input.rg}) {input.ref} {input.fastq_mod_R1} {input.fastq_mod_R2} | \
@@ -122,7 +122,7 @@ rule index_sorted_bams:
     group:
         "sorted_bam_stats_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -141,7 +141,7 @@ rule sorted_bam_stats:
     group:
         "sorted_bam_stats_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}

diff --git a/workflow/rules/3.1_bam_rmdup_realign_indels.smk b/workflow/rules/3.1_bam_rmdup_realign_indels.smk
@@ -56,7 +56,7 @@ rule merge_historical_bams_per_index:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/historical/" + REF_NAME + "/{sample}_{index}_merge_historical_bams_per_index.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -82,7 +82,7 @@ rule merge_modern_bams_per_index:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/modern/" + REF_NAME + "/{sample}_{index}_merge_modern_bams_per_index.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -106,7 +106,7 @@ rule index_merged_index_bams:
     group:
         "merged_index_bam_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -125,7 +125,7 @@ rule merged_index_bam_stats:
     group:
         "merged_index_bam_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -214,7 +214,7 @@ rule rmdup_historical_bams:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/historical/" + REF_NAME + "/{sample}_{index}_rmdup_historical_bams.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools view -@ {threads} -h {input.merged} | python3 workflow/scripts/samremovedup.py  | samtools view -b -o {output.rmdup} 2> {log}
@@ -253,7 +253,7 @@ rule index_rmdup_bams:
     group:
         "rmdup_bam_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -272,7 +272,7 @@ rule rmdup_bam_stats:
     group:
         "rmdup_bam_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -361,7 +361,7 @@ rule merge_historical_bams_per_sample:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/historical/" + REF_NAME + "/{sample}_merge_historical_bams_per_sample.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -387,7 +387,7 @@ rule merge_modern_bams_per_sample:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/modern/" + REF_NAME + "/{sample}_merge_modern_bams_per_sample.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -411,7 +411,7 @@ rule index_merged_sample_bams:
     group:
         "merged_sample_bam_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -430,7 +430,7 @@ rule merged_sample_bam_stats:
     group:
         "merged_sample_bam_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -566,7 +566,7 @@ rule index_realigned_bams:
     group:
         "realigned_bam_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -585,7 +585,7 @@ rule realigned_bam_stats:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/{dataset}/" + REF_NAME + "/{sample}_realigned_bam_stats.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -661,7 +661,7 @@ rule realigned_bam_depth:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/{dataset}/" + REF_NAME + "/{sample}_realigned_bam_depth.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         if [ {params.cov} = "True" ] # include sites with missing data / zero coverage

diff --git a/workflow/rules/3.2_historical_bam_mapDamage.smk b/workflow/rules/3.2_historical_bam_mapDamage.smk
@@ -55,7 +55,7 @@ rule index_rescaled_bams:
     group:
         "rescaled_bam_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -76,7 +76,7 @@ rule rescaled_bam_stats:
     log:
         "results/logs/3.2_historical_bam_mapDamage/" + REF_NAME + "/{sample}_rescaled_bam_stats.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}

diff --git a/workflow/rules/3.3_bam_subsampling.smk b/workflow/rules/3.3_bam_subsampling.smk
@@ -23,7 +23,7 @@ rule filter_bam_mapped_mq:
     log:
         "results/logs/3.3_bam_subsampling/{dataset}/" + REF_NAME + "/{sample}.{processed}_filter_bam_mapped_mq.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools view -h -b -F 4 -q 30 -@ {threads} -o {output.filtered} {input.bam} 2> {log}
@@ -43,7 +43,7 @@ rule subsample_bams:
     log:
         "results/logs/3.3_bam_subsampling/{dataset}/" + REF_NAME + "/{sample}.{processed}.subs_dp{DP}_subsample_bams.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         depth=`head -n 1 {input.dp} | cut -d' ' -f 1`
@@ -68,7 +68,7 @@ rule index_subsampled_bams:
     group:
         "subsampled_bam_group"
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -87,7 +87,7 @@ rule subsampled_bam_stats:
     log:
         "results/logs/3.3_bam_subsampling/{dataset}/" + REF_NAME + "/{sample}.{processed}.subs_dp{DP}_subsampled_bam_stats.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -114,7 +114,7 @@ rule subsampled_bam_depth:
     log:
         "results/logs/3.3_bam_subsampling/{dataset}/" + REF_NAME + "/{sample}.{processed}.subs_dp{DP}_subsampled_bam_depth.log",
     singularity:
-        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
+        "oras://community.wave.seqera.io/library/bwa_samtools_python:57d090a0dc055d93"
     shell:
         """
         if [ {params.cov} = "True" ] # include sites with missing data / zero coverage