Fix paths to container images

NBISweden · Nov 11, 2024 · b4c4fdc · b4c4fdc
1 parent f15f707
commit b4c4fdc
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Showing 10 changed files with 32 additions and 32 deletions.
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:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     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:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     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:
-        "community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
+        "oras://community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
     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:
-        "community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
+        "oras://community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
     shell:
         """
         bwa aln -l 16500 -n 0.01 -o 2 -t {threads} {input.ref} {input.R1_un} > {output.R1_sai} 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:
-        "community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
+        "oras://community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
     shell:
         """
         bwa mem {params.extra} -t {threads} {input.target} {input.fastq} | \
@@ -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:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     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:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     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:
-        "community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
+        "oras://community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
     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:
-        "community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
+        "oras://community.wave.seqera.io/library/bwa_samtools:2aa9aa78aef87695"
     shell:
         """
         bwa mem -M -t {threads} -R $(cat {input.rg}) {input.ref} {input.fastq_mod_R1} {input.fastq_mod_R2} | \

diff --git a/workflow/rules/5_CpG_identification.smk b/workflow/rules/5_CpG_identification.smk
@@ -128,7 +128,7 @@ rule merge_CpG_genotype_beds:
     log:
         "results/logs/5_CpG_identification/" + REF_NAME + "_merge_CpG_genotype_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -154,7 +154,7 @@ rule sort_CpG_genotype_beds:
     log:
         "results/logs/5_CpG_identification/" + REF_NAME + "_sort_CpG_genotype_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools sort -g {input.genomefile} -i {input.merged_bed} > {output.sorted_bed} 2> {log}
@@ -174,7 +174,7 @@ rule merge_all_CpG_beds:
     log:
         "results/logs/5_CpG_identification/" + REF_NAME + "_merge_all_CpG_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         files=`echo {input} | awk '{{print NF}}'`
@@ -200,7 +200,7 @@ rule sort_all_CpG_beds:
     log:
         "results/logs/5_CpG_identification/" + REF_NAME + "_sort_all_CpG_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools sort -g {input.genomefile} -i {input.merged_bed} > {output.sorted_bed} 2> {log}
@@ -217,7 +217,7 @@ rule make_noCpG_bed:
     log:
         "results/logs/5_CpG_identification/" + REF_NAME + ".no{CpG_method}_make_no_CpG_bed.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools subtract -a {input.ref_bed} -b {input.CpG_bed} > {output.no_CpG_bed} 2> {log}
@@ -238,7 +238,7 @@ rule merge_CpG_repeats_beds:
     log:
         "results/logs/5_CpG_identification/" + REF_NAME + ".{CpG_method}_merge_CpG_repeats_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         cat {input[0]} {input[1]} | sort -k1,1 -k2,2n > {output.tmp} 2> {log} &&
@@ -257,7 +257,7 @@ rule sort_CpG_repeats_beds:
     log:
         "results/logs/5_CpG_identification/" + REF_NAME + ".{CpG_method}_sort_CpG_repeats_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools sort -g {input.genomefile} -i {input.merged_bed} > {output.sorted_bed} 2> {log}
@@ -274,7 +274,7 @@ rule make_noCpG_repma_bed:
     log:
         "results/logs/5_CpG_identification/" + REF_NAME + ".no{CpG_method}_make_noCpG_repma_bed.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools subtract -a {input.ref_bed} -b {input.merged_bed} > {output.no_CpG_repma_bed} 2> {log}

diff --git a/workflow/rules/6_autosome_sexchromosome_bed_files.smk b/workflow/rules/6_autosome_sexchromosome_bed_files.smk
@@ -42,7 +42,7 @@ rule make_autosomes_bed:
     log:
         "results/logs/6_autosome_sexchromosome_bed_files/" + REF_NAME + "_make_autosomes_bed.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools subtract -a {input.ref_bed} -b {input.sexchr_bed} > {output.autosome_bed} 2> {log}
@@ -61,7 +61,7 @@ rule intersect_sexchr_repma_beds:
     log:
         "results/logs/6_autosome_sexchromosome_bed_files/" + REF_NAME + "_intersect_sexchr_repma_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools intersect -a {input.no_rep_bed} -b {input.sexchr_bed} > {output.repma_sex_chr} 2> {log}
@@ -80,7 +80,7 @@ rule intersect_autos_repma_beds:
     log:
         "results/logs/6_autosome_sexchromosome_bed_files/" + REF_NAME + "_intersect_autos_repma_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools intersect -a {input.no_rep_bed} -b {input.autosome_bed} > {output.repma_autos} 2> {log}
@@ -99,7 +99,7 @@ rule intersect_sexchr_noCpG_repma_beds:
     log:
         "results/logs/6_autosome_sexchromosome_bed_files/" + REF_NAME + ".no{CpG_method}_intersect_sexchr_noCpG_repma_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools intersect -a {input.no_CpG_repma_bed} -b {input.sexchr_bed} > {output.no_CpG_repma_sexchr} 2> {log}
@@ -118,7 +118,7 @@ rule intersect_autos_noCpG_repma_beds:
     log:
         "results/logs/6_autosome_sexchromosome_bed_files/" + REF_NAME + ".no{CpG_method}_intersect_autos_noCpG_repma_beds.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools intersect -a {input.no_CpG_repma_bed} -b {input.autosome_bed} > {output.no_CpG_repma_autos} 2> {log}

diff --git a/workflow/rules/7_mlRho.smk b/workflow/rules/7_mlRho.smk
@@ -362,7 +362,7 @@ rule bam2pro_autos:
     log:
         "results/logs/7_mlRho/{dataset}/" + REF_NAME + "/{sample}.{processed}_bam2pro_autos.log",
     singularity:
-        "community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
+        "oras://community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
     shell:
         """
         minDP=`head -n 1 {input.dp} | cut -d' ' -f 2`
@@ -396,7 +396,7 @@ rule mlRho_autos:
     log:
         "results/logs/7_mlRho/{dataset}/" + REF_NAME + "/{sample}.{processed}_mlRho_autos.log",
     singularity:
-        "community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
+        "oras://community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
     shell:
         """
         minDP=`head -n 1 {input.dp} | cut -d' ' -f 2`
@@ -427,7 +427,7 @@ rule bam2pro_sexchr:
     log:
         "results/logs/7_mlRho/{dataset}/" + REF_NAME + "/{sample}.{processed}_bam2pro_sexchr.log",
     singularity:
-        "community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
+        "oras://community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
     shell:
         """
         minDP=`head -n 1 {input.dp} | cut -d' ' -f 2`
@@ -461,7 +461,7 @@ rule mlRho_sexchr:
     log:
         "results/logs/7_mlRho/{dataset}/" + REF_NAME + "/{sample}.{processed}_mlRho_sexchr.log",
     singularity:
-        "community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
+        "oras://community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
     shell:
         """
         minDP=`head -n 1 {input.dp} | cut -d' ' -f 2`
@@ -492,7 +492,7 @@ rule bam2pro_genome:
     log:
         "results/logs/7_mlRho/{dataset}/" + REF_NAME + "/{sample}.{processed}_bam2pro_genome.log",
     singularity:
-        "community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
+        "oras://community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
     shell:
         """
         minDP=`head -n 1 {input.dp} | cut -d' ' -f 2`
@@ -526,7 +526,7 @@ rule mlRho_genome:
     log:
         "results/logs/7_mlRho/{dataset}/" + REF_NAME + "/{sample}.{processed}_mlRho_genome.log",
     singularity:
-        "community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
+        "oras://community.wave.seqera.io/library/mlrho_samtools:f1b883982ae4586d"
     shell:
         """
         minDP=`head -n 1 {input.dp} | cut -d' ' -f 2`

diff --git a/workflow/rules/8.1_vcf_CpG_filtering.smk b/workflow/rules/8.1_vcf_CpG_filtering.smk
@@ -107,7 +107,7 @@ rule remove_CpG_vcf:
     log:
         "results/logs/8.1_vcf_CpG_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}.no{CpG_method}_remove_CpG_vcf.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools intersect -a {input.vcf} -b {input.bed} -header -sorted -g {input.genomefile} | bgzip -c > {output.filtered} 2> {log}

diff --git a/workflow/rules/8.2_vcf_qual_repeat_filtering.smk b/workflow/rules/8.2_vcf_qual_repeat_filtering.smk
@@ -367,7 +367,7 @@ rule remove_repeats_vcf:
     log:
         "results/logs/8.2_vcf_qual_repeat_filtering/{dataset}/" + REF_NAME + "/{sample}.{processed}_remove_repeats_vcf.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools intersect -a {input.vcf} -b {input.bed} -header -sorted -g {input.genomefile} | bgzip -c > {output.filtered} 2> {log}

diff --git a/workflow/rules/9_merge_vcfs.smk b/workflow/rules/9_merge_vcfs.smk
@@ -517,7 +517,7 @@ rule filtered_vcf2bed:
     log:
         "results/logs/9_merge_vcfs/" + REF_NAME + ".all_fmissing{fmiss}.{chr}_filtered_vcf2bed.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         gzip -cd {input.vcf} | grep -v "^#" | awk -F'\t' '{{print $1, $2-1, $2}}' OFS='\t' > {output.bed} 2> {log}
@@ -661,7 +661,7 @@ rule filter_biallelic_missing_vcf:
     log:
         "results/logs/9_merge_vcfs/{dataset}/" + REF_NAME + "/{sample}.{processed}_fmissing{fmiss}.{chr}_filter_biallelic_missing_vcf.log",
     singularity:
-        "community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
+        "oras://community.wave.seqera.io/library/bedtools_htslib:62540682b559998a"
     shell:
         """
         bedtools intersect -a {input.vcf} -b {input.bed} -header -sorted -g {input.genomefile} | bgzip -c > {output.filtered} 2> {log}