Switch to version 1.20 from seqera

NBISweden · Jun 14, 2024 · 1e9a163 · 1e9a163
1 parent 801fd7d
commit 1e9a163
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Showing 7 changed files with 32 additions and 32 deletions.
diff --git a/utilities/mutational_load_snpeff/Snakefile b/utilities/mutational_load_snpeff/Snakefile
@@ -60,7 +60,7 @@ rule extract_number_of_samples:
     log:
         os.path.abspath("logs/rule_logs/extract_number_of_samples.log"),
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     threads: 2
     shell:
         """

diff --git a/workflow/rules/11_ROH.smk b/workflow/rules/11_ROH.smk
@@ -72,7 +72,7 @@ rule compress_roh_vcf:
     log:
         "results/logs/11_ROH/{dataset}/" + REF_NAME + ".{dataset}_fmissing{fmiss}.{chr}_compress_roh_vcf.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools view -Oz -o {output.compressed} {input.vcf} 2> {log} &&

diff --git a/workflow/rules/4_genotyping.smk b/workflow/rules/4_genotyping.smk
@@ -25,7 +25,7 @@ rule variant_calling:
     log:
         "results/logs/4_genotyping/{dataset}/" + REF_NAME + "/{sample}.{processed}_variant_calling.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools mpileup -Ou -Q 30 -q 30 -B -f {input.ref} {input.bam} | bcftools call -c -M -O b --threads {threads} -o {output.bcf} 2> {log}
@@ -43,7 +43,7 @@ rule sort_vcfs:
     log:
         "results/logs/4_genotyping/{dataset}/" + REF_NAME + "/{sample}.{processed}_sort_vcfs.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools sort -O b -T {params.tmpdir} -o {output.sort} {input.bcf} 2> {log}
@@ -61,7 +61,7 @@ rule index_sorted_vcfs:
     log:
         "results/logs/4_genotyping/{dataset}/" + REF_NAME + "/{sample}.{processed}_index_sorted_vcfs.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools index -o {output.index} {input.sort} 2> {log}
@@ -80,7 +80,7 @@ rule sorted_vcf_stats:
     log:
         "results/logs/4_genotyping/{dataset}/" + REF_NAME + "/{sample}.{processed}_sorted_vcf_stats.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools stats {input.sort} > {output.stats} 2> {log}

diff --git a/workflow/rules/5_CpG_identification.smk b/workflow/rules/5_CpG_identification.smk
@@ -76,7 +76,7 @@ rule sorted_bcf2vcf_CpG_id:
     log:
         "results/logs/5_CpG_identification/{dataset}/" + REF_NAME + "/{sample}.{processed}_sorted_bcf2vcf_CpG_id.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools convert -O z -o {output.vcf} {input.bcf} 2> {log}

diff --git a/workflow/rules/8.1_vcf_CpG_filtering.smk b/workflow/rules/8.1_vcf_CpG_filtering.smk
@@ -88,7 +88,7 @@ rule sorted_bcf2vcf_CpG_removal:
     log:
         "results/logs/8.1_vcf_CpG_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_sorted_bcf2vcf_CpG_removal.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools convert -O z -o {output.vcf} {input.bcf} 2> {log}
@@ -124,7 +124,7 @@ rule CpG_vcf2bcf:
     log:
         "results/logs/8.1_vcf_CpG_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}.no{CpG_method}_CpG_vcf2bcf.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools convert -O b -o {output.bcf} {input.filtered} 2> {log}
@@ -142,7 +142,7 @@ rule index_CpG_bcf:
     log:
         "results/logs/8.1_vcf_CpG_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}.no{CpG_method}_index_CpG_bcf.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools index -o {output.index} {input.bcf} 2> {log}
@@ -161,7 +161,7 @@ rule CpG_filtered_vcf_stats:
     log:
         "results/logs/8.1_vcf_CpG_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}.no{CpG_method}_CpG_filtered_vcf_stats.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools stats {input.bcf} > {output.stats} 2> {log}

diff --git a/workflow/rules/8.2_vcf_qual_repeat_filtering.smk b/workflow/rules/8.2_vcf_qual_repeat_filtering.smk
@@ -208,7 +208,7 @@ rule remove_snps_near_indels:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_remove_snps_near_indels.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools filter -g 5 -O b --threads {threads} -o {output.snps} {input.bcf} 2> {log}
@@ -228,7 +228,7 @@ rule filter_vcfs_qual_dp:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_filter_vcfs_qual_dp.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         minDP=`head -n 1 {input.dp} | cut -d' ' -f 2`
@@ -256,7 +256,7 @@ rule filter_vcfs_allelic_balance:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_filter_vcfs_allelic_balance.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools view -e 'GT="0/1" & (DP4[2]+DP4[3])/(DP4[0]+DP4[1]+DP4[2]+DP4[3]) < 0.2' {input.bcf} | \
@@ -275,7 +275,7 @@ rule index_filtered_vcfs:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_index_filtered_vcfs.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools index -o {output.index} {input.bcf} 2> {log}
@@ -294,7 +294,7 @@ rule filtered_vcf_stats:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_filtered_vcf_stats.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools stats {input.bcf} > {output.stats} 2> {log}
@@ -348,7 +348,7 @@ rule filtered_bcf2vcf:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_filtered_bcf2vcf.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools convert -O z -o {output.vcf} {input.bcf} 2> {log}
@@ -384,7 +384,7 @@ rule filtered_vcf2bcf:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_filtered_vcf2bcf.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools convert -O b -o {output.bcf} {input.filtered} 2> {log}
@@ -402,7 +402,7 @@ rule index_repmasked_vcfs:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_index_repmasked_vcfs.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools index -o {output.index} {input.bcf} 2> {log}
@@ -421,7 +421,7 @@ rule repmasked_vcf_stats:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_repmasked_vcf_stats.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools stats {input.bcf} > {output.stats} 2> {log}

diff --git a/workflow/rules/9_merge_vcfs.smk b/workflow/rules/9_merge_vcfs.smk
@@ -315,7 +315,7 @@ rule merge_all_vcfs:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + "_merge_all_vcfs.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         files=`echo {input.bcf} | awk '{{print NF}}'`
@@ -340,7 +340,7 @@ rule index_merged_vcf:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".all_index_merged_vcfs.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools index -o {output.index} {input.bcf} 2> {log}
@@ -359,7 +359,7 @@ rule merged_vcf_stats:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".all_merged_vcf_stats.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools stats {input.merged} > {output.stats} 2> {log}
@@ -400,7 +400,7 @@ rule filter_vcf_biallelic:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".all_filter_vcf_biallelic.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools view -m2 -M2 -v snps -Ob -o {output.bcf} {input.bcf} 2> {log} &&
@@ -420,7 +420,7 @@ rule biallelic_filtered_vcf_stats:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".all_biallelic_filtered_vcf_stats.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools stats {input.bcf} > {output.stats} 2> {log}
@@ -462,7 +462,7 @@ rule filter_vcf_missing:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".all_fmissing{fmiss}_filter_vcf_missing.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         # only include sites with zero missing data
@@ -496,7 +496,7 @@ rule remove_chromosomes:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".all_fmissing{fmiss}.autos_remove_chromosomes.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools view {input.bcf} \
@@ -535,7 +535,7 @@ rule extract_historical_samples:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".historical_fmissing{fmiss}.{chr}_extract_historical_samples.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     params:
         samples=hist_sm,
         all_samples=ALL_SAMPLES,
@@ -568,7 +568,7 @@ rule extract_modern_samples:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".modern_fmissing{fmiss}.{chr}_extract_modern_samples.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     params:
         samples=mod_sm,
         all_samples=ALL_SAMPLES,
@@ -600,7 +600,7 @@ rule missingness_filtered_vcf_stats:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".{dataset}_fmissing{fmiss}.{chr}_missingness_filtered_vcf_stats.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools stats {input.merged} > {output.stats} 2> {log}
@@ -642,7 +642,7 @@ rule repmasked_bcf2vcf:
     log:
         "results/logs/9_merge_vcfs/{dataset}/" + REF_NAME + "/{sample}.{processed}_repmasked_bcf2vcf.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools convert -O z -o {output.vcf} {input.bcf} 2> {log}
@@ -677,7 +677,7 @@ rule biallelic_missing_filtered_vcf_stats:
     log:
         "results/logs/9_merge_vcfs/{dataset}/" + REF_NAME + "/{sample}.{processed}_fmissing{fmiss}.{chr}_biallelic_missing_filtered_vcf_stats.log",
     singularity:
-        "docker://quay.io/biocontainers/bcftools:1.9--h68d8f2e_9"
+        "oras://community.wave.seqera.io/library/bcftools:1.20--f18ddc693c3747b4"
     shell:
         """
         bcftools stats {input.filtered} > {output.stats} 2> {log}