deps: add containers

Snakefile

@@ -17,6 +17,11 @@ OUT = config["output_dir"]
 localrules:
     all,
     aggregate_species,
+    copy_sample_bam,
+    copy_ref,
+    prepare_ab_table,
+    generate_ab_table_header,
+    mtb_filter_res_table_positions,
 
 
 include: "workflow/rules/choose_species.smk"

workflow/rules/mtb_prepare_files.smk

@@ -16,6 +16,8 @@ rule index_sample_bam:
         bam=OUT + "/mtb_typing/prepared_files/{sample}.bam",
     output:
         bai=temp(OUT + "/mtb_typing/prepared_files/{sample}.bam.bai"),
+    container:
+        "docker://staphb/samtools:1.17"
     conda:
         "../envs/gatk_picard.yaml"
     log:
@@ -118,6 +120,8 @@ rule prepare_snpeff_config:
         config=temp(OUT + "/mtb_typing/prepared_reference_data/{sample}/snpeff.config"),
     conda:
         "../envs/biopython.yaml"
+    container:
+        "docker://pegi3s/biopython:1.78"
     log:
         OUT + "/log/prepare_snpeff_config/{sample}.log",
     shell:
@@ -137,6 +141,8 @@ rule build_snpeff_db:
         touch(OUT + "/mtb_typing/prepared_reference_data/{sample}/build_snpeff_db.done"),
     conda:
         "../envs/snpeff.yaml"
+    container:
+        "docker://staphb/snpeff:5.1"
     log:
         OUT + "/log/build_snpeff_db/{sample}.log",
     shell:
@@ -185,6 +191,8 @@ rule compress_index_ab_table:
         index=OUT + "/mtb_typing/prepared_reference_data/{sample}/ab_table.tab.gz.tbi",
     conda:
         "../envs/bcftools.yaml"
+    container:
+        "docker://staphb/bcftools:1.16"
     log:
         OUT + "/log/compress_index_ab_table/{sample}.log",
     shell:

workflow/rules/mtb_typing.smk

@@ -5,6 +5,8 @@ rule mtb_lineage_id:
         tsv=OUT + "/mtb_typing/lineage_call/{sample}.tsv",
     conda:
         "../envs/fast_lineage_caller.yaml"
+    container:
+        "docker://ghcr.io/boasvdp/fast_lineage_caller:1.0.0"
     log:
         OUT + "/log/mtb_lineage_id/{sample}.log",
     message:
@@ -33,6 +35,8 @@ rule mtb_coll_contamination:
         tsv=OUT + "/mtb_typing/contamination_check/coll_positions/{sample}.tsv",
     conda:
         "../envs/gatk_picard.yaml"
+    container:
+        "docker://broadinstitute/gatk:4.3.0.0"
     log:
         OUT + "/log/mtb_typing/mtb_coll_contamination/{sample}.log",
     shell:
@@ -53,6 +57,8 @@ rule mtb_rrs_rrl_contamination:
         tsv=OUT + "/mtb_typing/contamination_check/rrs_rrl_contamination/{sample}.tsv",
     conda:
         "../envs/gatk_picard.yaml"
+    container:
+        "docker://broadinstitute/gatk:4.3.0.0"
     log:
         OUT + "/log/mtb_typing/mtb_rrs_rrl_contamination/{sample}.log",
     shell:
@@ -75,6 +81,8 @@ rule mtb_snpeff_annotation:
         stats=OUT + "/mtb_typing/snpeff_stats/{sample}.html",
     conda:
         "../envs/snpeff.yaml"
+    container:
+        "docker://staphb/snpeff:5.1"
     # params:
     #     outdir = OUT,
     #     db_dir_base = "snpeff_ref"
@@ -98,6 +106,8 @@ rule mtb_annotate_ab_positions:
         vcf=OUT + "/mtb_typing/annotated_vcf/{sample}.vcf",
     conda:
         "../envs/bcftools.yaml"
+    container:
+        "docker://staphb/bcftools:1.16"
     params:
         base_annotations="CHROM,POS",
         extra_annotations=lambda wildcards: SAMPLES[wildcards.sample][
@@ -124,6 +134,8 @@ rule mtb_annotated_vcf_to_table:
         tsv=OUT + "/mtb_typing/annotated_variants/{sample}.tsv",
     conda:
         "../envs/gatk_picard.yaml"
+    container:
+        "docker://broadinstitute/gatk:4.3.0.0"
     params:
         metadata=lambda wildcards: SAMPLES[wildcards.sample][
             "resistance_variants_columns"