Merge pull request #177 from ctmrbio/migrate-to-ghcr-singularity

Use GHCR for Singularity

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
 

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"

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

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:

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:

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:

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:

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:

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:

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:

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:

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 \

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:

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:

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:

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 \