diff --git a/CHANGELOG.md b/CHANGELOG.md index 5698243..4ce6851 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -38,12 +38,14 @@ situations. - Fixed typo in count summary output filenames for BBMap. - Increased time allocations for host removal in `ctmr_gandalf` cluster config. - Limited job allocations to one node in `ctmr_gandalf` cluster config. +- Fixed bug where unspecified kraken2 database did not raise expected WorkflowError. ### Changed - Updated Kraken2 to 2.1.2 and added `--minimum-hit-groups` argument in config file. - Updated fastp to 0.23.0. - Updated Kaiju to 1.8.2. - Updated BBMap to 38.93. +- Updated MultiQC to 1.11. ### Removed diff --git a/Snakefile b/Snakefile index 35fae51..42ba029 100644 --- a/Snakefile +++ b/Snakefile @@ -20,6 +20,7 @@ from scripts.common import UserMessages user_messages = UserMessages() stag_version = "0.5.0" +singularity_branch_tag = "-develop" # Replace with "-master" before publishing new version configfile: "config.yaml" report: "report/workflow.rst" diff --git a/envs/stag-mwc.yaml b/envs/stag-mwc.yaml index e197e2e..270b80a 100644 --- a/envs/stag-mwc.yaml +++ b/envs/stag-mwc.yaml @@ -12,7 +12,7 @@ dependencies: - bracken =2.5 - krona =2.7 - matplotlib =3.1.1 - - multiqc =1.8 + - multiqc =1.11 - pandas =1.2.1 - seaborn =0.9.0 - subread =1.6.0 diff --git a/rules/antibiotic_resistance/amrplusplus.smk b/rules/antibiotic_resistance/amrplusplus.smk index 7a1be6a..612cb45 100644 --- a/rules/antibiotic_resistance/amrplusplus.smk +++ b/rules/antibiotic_resistance/amrplusplus.smk @@ -46,7 +46,7 @@ rule get_local_megares: shadow: "shallow" singularity: - "shub://meglab-metagenomics/amrplusplus_v2" + "oras://ghcr.io/ctmrbio/stag-mwc:amrplusplus"+singularity_branch_tag params: megares_db=amrplusplus_config["megares"]["fasta"] or f"{MEGARES_FASTA}" shell: @@ -73,7 +73,7 @@ rule build_amr_index: conda: "../../envs/amrplusplus.yaml" singularity: - "shub://meglab-metagenomics/amrplusplus_v2" + "oras://ghcr.io/ctmrbio/stag-mwc:amrplusplus"+singularity_branch_tag shell: """ bwa index {input.megares_db} \ @@ -101,7 +101,7 @@ rule align_to_amr: conda: "../../envs/amrplusplus.yaml" singularity: - "shub://meglab-metagenomics/amrplusplus_v2" + "oras://ghcr.io/ctmrbio/stag-mwc:amrplusplus"+singularity_branch_tag threads: cluster_config["align_to_amr"]["n"] if "align_to_amr" in cluster_config else 10 params: @@ -134,7 +134,7 @@ rule run_resistome: conda: "../../envs/amrplusplus.yaml" singularity: - "shub://meglab-metagenomics/amrplusplus_v2" + "oras://ghcr.io/ctmrbio/stag-mwc:amrplusplus"+singularity_branch_tag params: script="scripts/amrplusplus/resistome", threshold=amrplusplus_config["resistome"]["threshold"], @@ -174,7 +174,7 @@ rule run_rarefaction: conda: "../../envs/amrplusplus.yaml" singularity: - "shub://meglab-metagenomics/amrplusplus_v2" + "oras://ghcr.io/ctmrbio/stag-mwc:amrplusplus"+singularity_branch_tag params: megares_db=amrplusplus_config["megares"]["fasta"] or f"{MEGARES_FASTA}", megares_annot=amrplusplus_config["megares"]["annotation"] or f"{MEGARES_ANNOT}", @@ -219,7 +219,7 @@ rule resistome_results: conda: "../../envs/amrplusplus.yaml" singularity: - "shub://meglab-metagenomics/amrplusplus_v2" + "oras://ghcr.io/ctmrbio/stag-mwc:amrplusplus"+singularity_branch_tag params: script="scripts/amrplusplus/amr_long_to_wide.py" shell: diff --git a/rules/antibiotic_resistance/groot.smk b/rules/antibiotic_resistance/groot.smk index 54c7532..9556d02 100644 --- a/rules/antibiotic_resistance/groot.smk +++ b/rules/antibiotic_resistance/groot.smk @@ -38,7 +38,7 @@ rule create_groot_index: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: dbdir=DBDIR/"groot/", db=groot_config["db"], @@ -79,7 +79,7 @@ rule groot_align: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: cluster_config["groot_align"]["n"] if "groot_align" in cluster_config else 8 params: @@ -120,7 +120,7 @@ rule groot_report: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: 1 params: diff --git a/rules/assembly/metawrap.smk b/rules/assembly/metawrap.smk index 878bf54..dcf4ae5 100644 --- a/rules/assembly/metawrap.smk +++ b/rules/assembly/metawrap.smk @@ -47,7 +47,7 @@ rule assembly: conda: "../../envs/assembly.yaml" singularity: - "shub://ctmrbio/stag-mwc:assembly" + "oras://ghcr.io/ctmrbio/stag-mwc:assembly"+singularity_branch_tag threads: cluster_config["assembly"]["n"] if "assembly" in cluster_config else 20 params: @@ -86,7 +86,7 @@ rule binning: conda: "../../envs/assembly.yaml" singularity: - "shub://ctmrbio/stag-mwc:assembly" + "oras://ghcr.io/ctmrbio/stag-mwc:assembly"+singularity_branch_tag threads: cluster_config["binning"]["n"] if "binning" in cluster_config else 20 params: @@ -127,7 +127,7 @@ rule consolidate_bins: conda: "../../envs/assembly.yaml" singularity: - "shub://ctmrbio/stag-mwc:assembly" + "oras://ghcr.io/ctmrbio/stag-mwc:assembly"+singularity_branch_tag threads: cluster_config["consolidate_bins"]["n"] if "consolidate_bins" in cluster_config else 20 params: @@ -165,7 +165,7 @@ rule blobology: conda: "../../envs/assembly.yaml" singularity: - "shub://ctmrbio/stag-mwc:assembly" + "oras://ghcr.io/ctmrbio/stag-mwc:assembly"+singularity_branch_tag threads: cluster_config["blobology"]["n"] if "blobology" in cluster_config else 20 params: diff --git a/rules/functional_profiling/humann.smk b/rules/functional_profiling/humann.smk index 90908d4..2a26745 100644 --- a/rules/functional_profiling/humann.smk +++ b/rules/functional_profiling/humann.smk @@ -53,7 +53,7 @@ rule humann: conda: "../../envs/humann.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: cluster_config["humann"]["n"] if "humann" in cluster_config else 20 params: @@ -102,7 +102,7 @@ rule normalize_humann_tables: conda: "../../envs/humann.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: 1 params: @@ -150,7 +150,7 @@ rule humann_join_tables: conda: "../../envs/humann.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: 1 params: diff --git a/rules/mappers/bbmap.smk b/rules/mappers/bbmap.smk index fa112a1..6726c40 100644 --- a/rules/mappers/bbmap.smk +++ b/rules/mappers/bbmap.smk @@ -69,7 +69,7 @@ for bbmap_config in config["bbmap"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: cluster_config["bbmap"]["n"] if "bbmap" in cluster_config else 8 params: @@ -116,7 +116,7 @@ for bbmap_config in config["bbmap"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: 1 params: @@ -154,7 +154,7 @@ for bbmap_config in config["bbmap"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: 4 params: diff --git a/rules/mappers/bowtie2.smk b/rules/mappers/bowtie2.smk index 4d72049..31947fb 100644 --- a/rules/mappers/bowtie2.smk +++ b/rules/mappers/bowtie2.smk @@ -88,7 +88,7 @@ for bt2_config in config["bowtie2"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ pileup.sh \ @@ -123,7 +123,7 @@ for bt2_config in config["bowtie2"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: 1 params: @@ -161,7 +161,7 @@ for bt2_config in config["bowtie2"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: 4 params: diff --git a/rules/multiqc/multiqc.smk b/rules/multiqc/multiqc.smk index f232395..26551ef 100644 --- a/rules/multiqc/multiqc.smk +++ b/rules/multiqc/multiqc.smk @@ -19,7 +19,7 @@ if config["multiqc_report"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: 1 params: diff --git a/rules/naive/bbcountunique.smk b/rules/naive/bbcountunique.smk index af4d118..d3b3664 100644 --- a/rules/naive/bbcountunique.smk +++ b/rules/naive/bbcountunique.smk @@ -31,7 +31,7 @@ if config["naive"]["assess_depth"]: conda: "../../envs/stag-mwc.yaml", singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: interval=config["bbcountunique"]["interval"] shell: diff --git a/rules/naive/sketch_compare.smk b/rules/naive/sketch_compare.smk index ae5318e..aa8d034 100644 --- a/rules/naive/sketch_compare.smk +++ b/rules/naive/sketch_compare.smk @@ -30,7 +30,7 @@ rule sketch: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: cluster_config["sketch"]["n"] if "sketch" in cluster_config else 4 shell: @@ -57,7 +57,7 @@ rule compare_sketches: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ comparesketch.sh \ @@ -84,7 +84,7 @@ rule plot_sample_similarity: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ scripts/plot_sketch_comparison_heatmap.py \ diff --git a/rules/preproc/host_removal.smk b/rules/preproc/host_removal.smk index 8637a57..56377ca 100644 --- a/rules/preproc/host_removal.smk +++ b/rules/preproc/host_removal.smk @@ -47,7 +47,7 @@ if config["host_removal"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: cluster_config["remove_host"]["n"] if "remove_host" in cluster_config else 8 params: @@ -101,7 +101,7 @@ if config["host_removal"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: 1 shell: diff --git a/rules/preproc/preprocessing_summary.smk b/rules/preproc/preprocessing_summary.smk index f3fece9..5f7be08 100644 --- a/rules/preproc/preprocessing_summary.smk +++ b/rules/preproc/preprocessing_summary.smk @@ -35,7 +35,7 @@ rule preprocessing_summary: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: 1 shell: diff --git a/rules/preproc/read_quality.smk b/rules/preproc/read_quality.smk index a9e1909..555e646 100644 --- a/rules/preproc/read_quality.smk +++ b/rules/preproc/read_quality.smk @@ -33,7 +33,7 @@ if config["qc_reads"]: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: cluster_config["fastp"]["n"] if "fastp" in cluster_config else 4 params: diff --git a/rules/taxonomic_profiling/kaiju.smk b/rules/taxonomic_profiling/kaiju.smk index 90a618e..084a52d 100644 --- a/rules/taxonomic_profiling/kaiju.smk +++ b/rules/taxonomic_profiling/kaiju.smk @@ -74,7 +74,7 @@ rule kaiju: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: db=kaiju_config["db"], nodes=kaiju_config["nodes"], @@ -115,7 +115,7 @@ rule kaiju2krona: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ kaiju2krona \ @@ -136,7 +136,7 @@ rule create_kaiju_krona_plot: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ ktImportText \ @@ -159,7 +159,7 @@ rule kaiju_report: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ kaiju2table \ @@ -190,7 +190,7 @@ rule join_kaiju_reports: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ scripts/join_tables.py \ @@ -214,7 +214,7 @@ rule kaiju_area_plot: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ scripts/area_plot.py \ diff --git a/rules/taxonomic_profiling/kraken2.smk b/rules/taxonomic_profiling/kraken2.smk index 9b620d1..fced947 100644 --- a/rules/taxonomic_profiling/kraken2.smk +++ b/rules/taxonomic_profiling/kraken2.smk @@ -25,7 +25,7 @@ localrules: kraken2_config = config["kraken2"] if config["taxonomic_profile"]["kraken2"]: - if not Path(kraken2_config["db"]).exists(): + if not (kraken2_config["db"] and Path(kraken2_config["db"]).exists()): err_message = "No Kraken2 database folder at: '{}'!\n".format(kraken2_config["db"]) err_message += "Specify the path in the kraken2 section of config.yaml.\n" err_message += "Run 'snakemake download_minikraken2' to download a copy into '{dbdir}'\n".format(dbdir=DBDIR/"kraken2") @@ -89,7 +89,7 @@ rule kraken2: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: db=kraken2_config["db"], confidence=kraken2_config["confidence"], @@ -124,7 +124,7 @@ rule kraken_mpa_style: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ kreport2mpa.py \ @@ -150,7 +150,7 @@ rule join_kraken2_mpa: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: value_column="reads", feature_column="taxon_name", @@ -177,7 +177,7 @@ rule kraken2_area_plot: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ scripts/area_plot.py \ @@ -202,7 +202,7 @@ rule combine_kreports: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ scripts/KrakenTools/combine_kreports.py \ @@ -227,7 +227,7 @@ rule kreport2krona: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ scripts/KrakenTools/kreport2krona.py \ @@ -249,7 +249,7 @@ rule create_kraken2_krona_plot: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ ktImportText \ @@ -306,7 +306,7 @@ rule bracken_kreport: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: kmer_distrib=kraken2_config["bracken"]["kmer_distrib"], thresh=kraken2_config["bracken"]["thresh"], @@ -338,7 +338,7 @@ rule bracken_all_levels: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: kmer_distrib=kraken2_config["bracken"]["kmer_distrib"], thresh=kraken2_config["bracken"]["thresh"], @@ -366,7 +366,7 @@ rule bracken_mpa_style: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ kreport2mpa.py \ @@ -392,7 +392,7 @@ rule join_bracken_mpa: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: value_column="reads", feature_column="taxon_name", @@ -419,7 +419,7 @@ rule bracken_area_plot: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ scripts/area_plot.py \ @@ -444,7 +444,7 @@ rule join_bracken: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: value_column="fraction_total_reads", feature_column="name", @@ -473,7 +473,7 @@ rule bracken2krona: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ scripts/KrakenTools/kreport2krona.py \ @@ -495,7 +495,7 @@ rule create_bracken_krona_plot: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ ktImportText \ @@ -516,7 +516,7 @@ rule filter_bracken: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: filter_bracken="scripts/KrakenTools/filter_bracken.out.py", include=kraken2_config["filter_bracken"]["include"], @@ -546,7 +546,7 @@ rule join_bracken_filtered: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag params: value_column="fraction_total_reads", feature_column="name", diff --git a/rules/taxonomic_profiling/metaphlan.smk b/rules/taxonomic_profiling/metaphlan.smk old mode 100755 new mode 100644 index dc994d9..2c80ec5 --- a/rules/taxonomic_profiling/metaphlan.smk +++ b/rules/taxonomic_profiling/metaphlan.smk @@ -45,7 +45,7 @@ rule metaphlan: conda: "../../envs/metaphlan.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: cluster_config["metaphlan"]["n"] if "metaphlan" in cluster_config else 5 params: @@ -108,7 +108,7 @@ rule combine_metaphlan_tables: conda: "../../envs/metaphlan.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: 1 shell: @@ -130,7 +130,7 @@ rule metaphlan_area_plot: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag shell: """ scripts/area_plot.py \ @@ -156,7 +156,7 @@ rule plot_metaphlan_heatmap: conda: "../../envs/stag-mwc.yaml" singularity: - "shub://ctmrbio/stag-mwc:stag-mwc" + "oras://ghcr.io/ctmrbio/stag-mwc:stag-mwc"+singularity_branch_tag threads: 1 params: @@ -196,7 +196,7 @@ rule create_metaphlan_krona_plots: conda: "../../envs/metaphlan.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: 1 shell: diff --git a/rules/taxonomic_profiling/strainphlan.smk b/rules/taxonomic_profiling/strainphlan.smk old mode 100755 new mode 100644 index 277a4ac..9948817 --- a/rules/taxonomic_profiling/strainphlan.smk +++ b/rules/taxonomic_profiling/strainphlan.smk @@ -45,7 +45,7 @@ rule consensus_markers: conda: "../../envs/metaphlan.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: cluster_config["strainphlan"]["n"] if "strainphlan" in cluster_config else 8 params: @@ -74,7 +74,7 @@ rule print_clades: conda: "../../envs/metaphlan.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: cluster_config["strainphlan"]["n"] if "strainphlan" in cluster_config else 8 params: @@ -109,7 +109,7 @@ rule extract_markers: conda: "../../envs/metaphlan.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: cluster_config["strainphlan"]["n"] if "strainphlan" in cluster_config else 8 params: @@ -142,7 +142,7 @@ rule strainphlan: conda: "../../envs/metaphlan.yaml" singularity: - "shub://AroArz/singularity_playground:biobakery" + "oras://ghcr.io/ctmrbio/stag-mwc:biobakery"+singularity_branch_tag threads: cluster_config["strainphlan"]["n"] if "strainphlan" in cluster_config else 8 params: