bump version to v0.10.4

CITATION.cff

@@ -17,6 +17,6 @@ authors:
     given-names: Ben J.
     orcid: https://orcid.org/0000-0003-0670-7480
 title: "Bin chicken: targeted recovery of low abundance metagenome assembled genomes through intelligent coassembly"
-version: 0.10.3
+version: 0.10.4
 doi: 10.5281/zenodo.10511708
-date-released: 2024-01-15
+date-released: 2024-04-08

binchicken/__init__.py

@@ -1 +1 @@
-__version__ = "0.10.3"
+__version__ = "0.10.4"

docs/tools/coassemble.md

@@ -25,7 +25,7 @@ binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --si
 # Create snakemake profile at ~/.config/snakemake/qsub with cluster, cluster-status, cluster-cancel, etc.
 # See https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles
 binchicken coassemble --forward reads_1.1.fq ... --reverse reads_1.2.fq ... --run-aviary \
-  --snakemake-profile qsub --cluster-retries 3 --local-cores 64 --cores 64
+  --snakemake-profile qsub --local-cores 64 --cores 64
 ```
 
 Important options:
@@ -42,8 +42,8 @@ Important options:
 - Differential-abundance binning samples for single-assembly can also be found (`--single-assembly`)
 - Snakemake profiles can be used to automatically submit jobs to HPC clusters (`--snakemake-profile`)
 
-Paired end reads of form reads_1.1.fq, reads_1_1.fq and reads_1_R1.fq are automatically detected and matched to their basename.
-Most intermediate files can be provided to skip those steps (see `binchicken coassemble --full-help`).
+Paired end reads of form reads_1.1.fq, reads_1_1.fq and reads_1_R1.fq, where reads_1 is the sample name are automatically detected and matched to their basename.
+Most intermediate files can be provided to skip intermediate steps (e.g. SingleM otu tables, read sizes or genome transcripts; see `binchicken coassemble --full-help`).
 
 # OPTIONS
 
@@ -226,15 +226,20 @@ Most intermediate files can be provided to skip those steps (see `binchicken coa
   Maximum percent alignment of mapped sequences kept for coassembly
     [default: 99%]
 
+**\--run-aviary**
+
+  Run Aviary commands for all identified coassemblies (unless specific
+    coassemblies are chosen with \--coassemblies) [default: do not]
+
 **\--aviary-speed** {fast,comprehensive}
 
   Run Aviary recover in \'fast\' or \'comprehensive\' mode. Fast mode
-    skips slow binners and refinement steps.
+    skips slow binners and refinement steps. [default: fast]
 
-**\--run-aviary**
+**\--assembly-strategy** {dynamic,metaspades,megahit}
 
-  Run Aviary commands for all identified coassemblies (unless
-    specified)
+  Assembly strategy to use with Aviary. [default: dynamic; attempts
+    metaspades and if fails, switches to megahit]
 
 **\--aviary-gtdbtk-db** *AVIARY_GTDBTK_DB*
 
@@ -246,14 +251,23 @@ Most intermediate files can be provided to skip those steps (see `binchicken coa
   Path to CheckM2 database directory for Aviary. [default: use path
     from CHECKM2DB env variable]
 
-**\--aviary-cores** *AVIARY_CORES*
+**\--aviary-assemble-cores** *AVIARY_ASSEMBLE_CORES*
+
+  Maximum number of cores for Aviary assemble to use. [default: 64]
+
+**\--aviary-assemble-memory** *AVIARY_ASSEMBLE_MEMORY*
+
+  Maximum amount of memory for Aviary assemble to use (Gigabytes).
+    [default: 500]
+
+**\--aviary-recover-cores** *AVIARY_RECOVER_CORES*
 
-  Maximum number of cores for Aviary to use. Half used for recovery.
+  Maximum number of cores for Aviary recover to use. [default: 32]
 
-**\--aviary-memory** *AVIARY_MEMORY*
+**\--aviary-recover-memory** *AVIARY_RECOVER_MEMORY*
 
-  Maximum amount of memory for Aviary to use (Gigabytes). Half used
-    for recovery
+  Maximum amount of memory for Aviary recover to use (Gigabytes).
+    [default: 250]
 
 # GENERAL OPTIONS
 
@@ -268,7 +282,7 @@ Most intermediate files can be provided to skip those steps (see `binchicken coa
 
 **\--cores** *CORES*
 
-  Maximum number of cores to use
+  Maximum number of cores to use [default: 1]
 
 **\--dryrun**
 
@@ -277,19 +291,19 @@ Most intermediate files can be provided to skip those steps (see `binchicken coa
 **\--snakemake-profile** *SNAKEMAKE_PROFILE*
 
   Snakemake profile (see
-    https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles).
+    https://snakemake.readthedocs.io/en/v7.32.3/executing/cli.html#profiles).
     Can be used to submit rules as jobs to cluster engine (see
-    https://snakemake.readthedocs.io/en/stable/executing/cluster.html).
+    https://snakemake.readthedocs.io/en/v7.32.3/executing/cluster.html).
 
 **\--local-cores** *LOCAL_CORES*
 
   Maximum number of cores to use on localrules when running in cluster
-    mode
+    mode [default: 1]
 
 **\--cluster-retries** *CLUSTER_RETRIES*
 
   Number of times to retry a failed job when using cluster submission
-    (see \`\--snakemake-profile\`).
+    (see \`\--snakemake-profile\`) [default: 3].
 
 **\--snakemake-args** *SNAKEMAKE_ARGS*
 

docs/tools/evaluate.md

@@ -8,10 +8,12 @@ Compares the recovery by phyla and by single-copy marker gene.
 
 ```bash
 # Example: evaluate a completed coassembly
-binchicken evaluate --coassemble-output coassemble_dir --aviary-outputs coassembly_0_dir ...
+binchicken evaluate --coassemble-output coassemble_dir \
+    --aviary-outputs coassembly_0_dir ...
 
 # Example: evaluate a completed coassembly by providing genomes directly
-binchicken evaluate --coassemble-output coassemble_dir --new-genomes genome_1.fna ... --coassembly-run coassembly_0
+binchicken evaluate --coassemble-output coassemble_dir \
+    --new-genomes genome_1.fna ... --coassembly-run coassembly_0
 ```
 
 Defaults to using genomes (from the provided coassemble outputs) with at least 70% complete and at most 10% contamination as estimated by CheckM2.
@@ -42,7 +44,7 @@ Defaults to using genomes (from the provided coassemble outputs) with at least 7
 **\--coassemble-elusive-edges** *COASSEMBLE_ELUSIVE_EDGES*
 
   Elusive edges output from Bin chicken coassemble (alternative to
-    \--coassemble-output)
+    \--coassemble- output)
 
 **\--coassemble-elusive-clusters** *COASSEMBLE_ELUSIVE_CLUSTERS*
 
@@ -52,7 +54,7 @@ Defaults to using genomes (from the provided coassemble outputs) with at least 7
 **\--coassemble-summary** *COASSEMBLE_SUMMARY*
 
   Summary output from Bin chicken coassemble (alternative to
-    \--coassemble-output)
+    \--coassemble- output)
 
 **\--aviary-outputs** *AVIARY_OUTPUTS* [*AVIARY_OUTPUTS* \...]
 
@@ -72,7 +74,7 @@ Defaults to using genomes (from the provided coassemble outputs) with at least 7
 **\--coassembly-run** *COASSEMBLY_RUN*
 
   Name of coassembly run to produce new genomes (alternative to
-    \--aviary-outputs, also requires \--new-genomes)
+    \--aviary- outputs, also requires \--new-genomes)
 
 **\--singlem-metapackage** *SINGLEM_METAPACKAGE*
 
@@ -128,7 +130,7 @@ Defaults to using genomes (from the provided coassemble outputs) with at least 7
 
 **\--cores** *CORES*
 
-  Maximum number of cores to use
+  Maximum number of cores to use [default: 1]
 
 **\--dryrun**
 
@@ -137,24 +139,24 @@ Defaults to using genomes (from the provided coassemble outputs) with at least 7
 **\--snakemake-profile** *SNAKEMAKE_PROFILE*
 
   Snakemake profile (see
-    https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles).
+    https://snakemake.readthedocs.io/en/v7.32.3/executing/cli.html#profiles).
     Can be used to submit rules as jobs to cluster engine (see
-    https://snakemake.readthedocs.io/en/stable/executing/cluster.html).
+    https://snakemake.readthedocs.io/en/v7.32.3/executing/cluster.html).
 
 **\--local-cores** *LOCAL_CORES*
 
   Maximum number of cores to use on localrules when running in cluster
-    mode
+    mode [default: 1]
 
 **\--cluster-retries** *CLUSTER_RETRIES*
 
   Number of times to retry a failed job when using cluster submission
-    (see \`\--snakemake-profile\`).
+    (see \`\--snakemake-profile\`) [default: 3].
 
 **\--snakemake-args** *SNAKEMAKE_ARGS*
 
   Additional commands to be supplied to snakemake in the form of a
-    space-prefixed single string e.g. \" \--quiet\"
+    space- prefixed single string e.g. \" \--quiet\"
 
 **\--tmp-dir** *TMP_DIR*
 

docs/tools/iterate.md

@@ -11,7 +11,8 @@ All [coassemble](/tools/coassemble) options are available and can be altered for
 binchicken iterate --coassemble-output coassemble_dir
 
 # Example: rerun coassemble, adding new bins to database, providing genomes directly
-binchicken iterate --coassemble-output coassemble_dir --new-genomes new_genome_1.fna
+binchicken iterate --coassemble-output coassemble_dir \
+    --new-genomes new_genome_1.fna
 ```
 
 Defaults to using genomes (from the provided coassemble outputs) with at least 70% complete and at most 10% contamination as estimated by CheckM2.
@@ -23,7 +24,7 @@ Automatically excludes previous coassemblies.
 
 **\--iteration** *ITERATION*
 
-  Iteration number used for unique bin naming
+  Iteration number used for unique bin naming [default: 0]
 
 **\--aviary-outputs** *AVIARY_OUTPUTS* [*AVIARY_OUTPUTS* \...]
 
@@ -195,7 +196,7 @@ Automatically excludes previous coassemblies.
 
   Skip appraise to discover samples to differential abundance binning.
     Forces \--num-coassembly-samples and \--max-coassembly-samples to 1
-    and sets \--max-coassembly-size to None
+    and sets \--max- coassembly-size to None
 
 **\--exclude-coassemblies** *EXCLUDE_COASSEMBLIES* [*EXCLUDE_COASSEMBLIES* \...]
 
@@ -214,7 +215,7 @@ Automatically excludes previous coassemblies.
 **\--max-coassembly-samples** *MAX_COASSEMBLY_SAMPLES*
 
   Upper bound for number of samples per coassembly cluster [default:
-    \--num-coassembly-samples]
+    \--num- coassembly-samples]
 
 **\--max-coassembly-size** *MAX_COASSEMBLY_SIZE*
 
@@ -254,15 +255,20 @@ Automatically excludes previous coassemblies.
   Maximum percent alignment of mapped sequences kept for coassembly
     [default: 99%]
 
+**\--run-aviary**
+
+  Run Aviary commands for all identified coassemblies (unless specific
+    coassemblies are chosen with \--coassemblies) [default: do not]
+
 **\--aviary-speed** {fast,comprehensive}
 
   Run Aviary recover in \'fast\' or \'comprehensive\' mode. Fast mode
-    skips slow binners and refinement steps.
+    skips slow binners and refinement steps. [default: fast]
 
-**\--run-aviary**
+**\--assembly-strategy** {dynamic,metaspades,megahit}
 
-  Run Aviary commands for all identified coassemblies (unless
-    specified)
+  Assembly strategy to use with Aviary. [default: dynamic; attempts
+    metaspades and if fails, switches to megahit]
 
 **\--aviary-gtdbtk-db** *AVIARY_GTDBTK_DB*
 
@@ -274,14 +280,23 @@ Automatically excludes previous coassemblies.
   Path to CheckM2 database directory for Aviary. [default: use path
     from CHECKM2DB env variable]
 
-**\--aviary-cores** *AVIARY_CORES*
+**\--aviary-assemble-cores** *AVIARY_ASSEMBLE_CORES*
+
+  Maximum number of cores for Aviary assemble to use. [default: 64]
+
+**\--aviary-assemble-memory** *AVIARY_ASSEMBLE_MEMORY*
+
+  Maximum amount of memory for Aviary assemble to use (Gigabytes).
+    [default: 500]
+
+**\--aviary-recover-cores** *AVIARY_RECOVER_CORES*
 
-  Maximum number of cores for Aviary to use. Half used for recovery.
+  Maximum number of cores for Aviary recover to use. [default: 32]
 
-**\--aviary-memory** *AVIARY_MEMORY*
+**\--aviary-recover-memory** *AVIARY_RECOVER_MEMORY*
 
-  Maximum amount of memory for Aviary to use (Gigabytes). Half used
-    for recovery
+  Maximum amount of memory for Aviary recover to use (Gigabytes).
+    [default: 250]
 
 # GENERAL OPTIONS
 
@@ -296,7 +311,7 @@ Automatically excludes previous coassemblies.
 
 **\--cores** *CORES*
 
-  Maximum number of cores to use
+  Maximum number of cores to use [default: 1]
 
 **\--dryrun**
 
@@ -305,24 +320,24 @@ Automatically excludes previous coassemblies.
 **\--snakemake-profile** *SNAKEMAKE_PROFILE*
 
   Snakemake profile (see
-    https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles).
+    https://snakemake.readthedocs.io/en/v7.32.3/executing/cli.html#profiles).
     Can be used to submit rules as jobs to cluster engine (see
-    https://snakemake.readthedocs.io/en/stable/executing/cluster.html).
+    https://snakemake.readthedocs.io/en/v7.32.3/executing/cluster.html).
 
 **\--local-cores** *LOCAL_CORES*
 
   Maximum number of cores to use on localrules when running in cluster
-    mode
+    mode [default: 1]
 
 **\--cluster-retries** *CLUSTER_RETRIES*
 
   Number of times to retry a failed job when using cluster submission
-    (see \`\--snakemake-profile\`).
+    (see \`\--snakemake-profile\`) [default: 3].
 
 **\--snakemake-args** *SNAKEMAKE_ARGS*
 
   Additional commands to be supplied to snakemake in the form of a
-    space-prefixed single string e.g. \" \--quiet\"
+    space- prefixed single string e.g. \" \--quiet\"
 
 **\--tmp-dir** *TMP_DIR*