Merge pull request #87 from NBISweden/containers

Replace custom containers with seqera containers incl version upgrades
NBISweden · Nov 11, 2024 · 990ddcc · 990ddcc
2 parents 888ccf7 + 52f4afe
commit 990ddcc
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Showing 16 changed files with 58 additions and 142 deletions.
diff --git a/workflow/docker/bedtools-2.29.2/Dockerfile b/workflow/docker/bedtools-2.29.2/Dockerfile
diff --git a/workflow/docker/bwa/Dockerfile b/workflow/docker/bwa/Dockerfile
diff --git a/workflow/docker/htslib-1.15.1/Dockerfile b/workflow/docker/htslib-1.15.1/Dockerfile
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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools faidx {input.ref} 2> {log}

diff --git a/workflow/rules/0.2_repeat_identification.smk b/workflow/rules/0.2_repeat_identification.smk
@@ -123,7 +123,7 @@ rule sort_repeats_bed:
     log:
         "results/logs/0.2_repeat_identification/" + REF_NAME + "_sort_repeats_bed.log",
     singularity:
-        "docker://nbisweden/generode-bedtools-2.29.2"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:06ed4722f423d939"
     shell:
         """
         bedtools sort -g {input.genomefile} -i {input.rep_bed} > {output.sorted_rep_bed} 2> {log}
@@ -141,7 +141,7 @@ rule make_no_repeats_bed:
     log:
         "results/logs/0.2_repeat_identification/" + REF_NAME + "_make_no_repeats_bed.log",
     singularity:
-        "docker://nbisweden/generode-bedtools-2.29.2"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:06ed4722f423d939"
     shell:
         """
         bedtools subtract -a {input.ref_bed} -b {input.sorted_rep_bed} > {output.no_rep_bed} 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:
-        "docker://nbisweden/generode-bwa:latest"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://nbisweden/generode-bwa:latest"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -345,7 +345,7 @@ rule merged_mitogenome_bam_stats:
     group:
         "historical_merged_mito_bams_group"
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://nbisweden/generode-bwa:latest"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"  # This container includes python 3.7.6 with default python modules
+        "oras://community.wave.seqera.io/library/samtools_python:2e56d0f345426c81"
     shell:
         """
         if [ ! -d {output.fasta_dir} ]; then
@@ -696,7 +696,7 @@ rule split_vcf_files:
     log:
         "results/logs/13_GERP/{chr}_chunks/" + REF_NAME + "/{dataset}/vcf/{sample}.{processed}_fmissing{fmiss}.{chr}.{chunk}_split_vcf_chunks.log",
     singularity:
-        "docker://nbisweden/generode-bedtools-2.29.2"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:06ed4722f423d939"
     shell:
         """
         bedtools intersect -a {input.vcf} -b {input.chunk_bed} -g {input.genomefile} -header | gzip - > {output.vcf_chunk} 2> {log}
@@ -712,7 +712,7 @@ rule split_chunk_bed_files:
     log:
         "results/logs/13_GERP/" + REF_NAME + ".{chunk}_{chr}_split_chunk_bed_files.log",
     singularity:
-        "docker://nbisweden/generode-bedtools-2.29.2"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:06ed4722f423d939"
     shell:
         """
         bedtools makewindows -b {input.chunk_bed} -w 10000000 > {output.chunk_win_bed} 2> {log}

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:
-        "docker://nbisweden/generode-bwa:latest"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://nbisweden/generode-bwa:latest"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -141,7 +141,7 @@ rule sorted_bam_stats:
     group:
         "sorted_bam_stats_group"
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -106,7 +106,7 @@ rule index_merged_index_bams:
     group:
         "merged_index_bam_group"
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -125,7 +125,7 @@ rule merged_index_bam_stats:
     group:
         "merged_index_bam_group"
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -214,10 +214,11 @@ rule rmdup_historical_bams:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/historical/" + REF_NAME + "/{sample}_{index}_rmdup_historical_bams.log",
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/samtools_python:2e56d0f345426c81"
     shell:
         """
-        samtools view -@ {threads} -h {input.merged} | python3 workflow/scripts/samremovedup.py  | samtools view -b -o {output.rmdup} 2> {log}
+        samtools view -@ {threads} -h {input.merged} | python3 workflow/scripts/samremovedup.py | \
+        samtools view -b -o {output.rmdup} 2> {log}
         """
 
 
@@ -253,7 +254,7 @@ rule index_rmdup_bams:
     group:
         "rmdup_bam_group"
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -272,7 +273,7 @@ rule rmdup_bam_stats:
     group:
         "rmdup_bam_group"
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -361,7 +362,7 @@ 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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -387,7 +388,7 @@ 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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -411,7 +412,7 @@ rule index_merged_sample_bams:
     group:
         "merged_sample_bam_group"
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -430,7 +431,7 @@ rule merged_sample_bam_stats:
     group:
         "merged_sample_bam_group"
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -566,7 +567,7 @@ rule index_realigned_bams:
     group:
         "realigned_bam_group"
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools index {input.bam} {output.index} 2> {log}
@@ -585,7 +586,7 @@ rule realigned_bam_stats:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/{dataset}/" + REF_NAME + "/{sample}_realigned_bam_stats.log",
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}
@@ -661,7 +662,7 @@ rule realigned_bam_depth:
     log:
         "results/logs/3.1_bam_rmdup_realign_indels/{dataset}/" + REF_NAME + "/{sample}_realigned_bam_depth.log",
     singularity:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     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:
-        "docker://biocontainers/samtools:v1.9-4-deb_cv1"
+        "oras://community.wave.seqera.io/library/bwa_samtools:58df1856e12c14b9"
     shell:
         """
         samtools flagstat {input.bam} > {output.stats} 2> {log}