From 0c96c3def7f3eba0c3c24009b371de72e3b6d1d9 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Fri, 2 Feb 2024 13:19:10 +1100
Subject: [PATCH 1/7] Bump version number

---
 metaphor/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/metaphor/__init__.py b/metaphor/__init__.py
index 59b2527..de8b94c 100644
--- a/metaphor/__init__.py
+++ b/metaphor/__init__.py
@@ -2,7 +2,7 @@
 __email__ = "17276653+vinisalazar@users.noreply.github.com"
 __license__ = "MIT"
 __copyright__ = "The University of Melbourne 2023"
-__version__ = "1.7.10"
+__version__ = "1.7.11"
 
 __doc__ = """
 Metaphor top-level module. This is the entrypoint for the `cli`, `config`, and `workflow` packages.

From eee8b01f8781f3f61631f41d4c42dfd7733c5247 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Fri, 2 Feb 2024 13:19:41 +1100
Subject: [PATCH 2/7] Bump Pandas version

---
 metaphor/workflow/envs/python-utils.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/metaphor/workflow/envs/python-utils.yaml b/metaphor/workflow/envs/python-utils.yaml
index 33da6af..2fce9bd 100644
--- a/metaphor/workflow/envs/python-utils.yaml
+++ b/metaphor/workflow/envs/python-utils.yaml
@@ -4,7 +4,7 @@ channels:
   - bioconda
 dependencies:
   - biopython
-  - pandas>=2
+  - pandas>=2.1
   - python>=3.9
   - seaborn
   - seqstats  # This has to be here because assembly_report.py runs it from Python

From 07578fd55e3fb95e0684bb18198046a830d6a4e2 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 5 Mar 2024 09:53:40 +1100
Subject: [PATCH 3/7] Bump wrapper version

---
 metaphor/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/metaphor/__init__.py b/metaphor/__init__.py
index de8b94c..3f58b9f 100644
--- a/metaphor/__init__.py
+++ b/metaphor/__init__.py
@@ -13,7 +13,7 @@
 
 # Snakemake wrapper version
 # This should match the latest released tag on: https://github.com/snakemake/snakemake-wrappers
-wrapper_version = "v3.3.3"
+wrapper_version = "v3.4.1"
 wrapper_prefix = "https://github.com/snakemake/snakemake-wrappers/raw/"
 
 github_url = "https://github.com/vinisalazar/metaphor"

From f62fea5abe9ca32ba4221e6162852b512fb19561 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 5 Mar 2024 09:55:46 +1100
Subject: [PATCH 4/7] Add resources directive to fastqc rules

---
 metaphor/workflow/rules/qc.smk | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/metaphor/workflow/rules/qc.smk b/metaphor/workflow/rules/qc.smk
index 55f988d..6230d5f 100644
--- a/metaphor/workflow/rules/qc.smk
+++ b/metaphor/workflow/rules/qc.smk
@@ -108,6 +108,8 @@ rule fastqc_raw:  # qc on raw, unmerged reads
         html="output/qc/fastqc/{sample}-{unit}-{read}-raw.html",
     params:
         "--quiet",
+    resources:
+        mem_mb=10000 if get_max_mb(0.5) > 10000 else get_max_mb(0.5),
     wildcard_constraints:
         sample="|".join(sample_IDs),
         unit="|".join(unit_names),
@@ -127,6 +129,8 @@ rule fastqc_trimmed:  # qc on trimmed reads
     output:
         zip="output/qc/fastqc/{sample}-{unit}-{read}-trimmed_fastqc.zip",
         html="output/qc/fastqc/{sample}-{unit}-{read}-trimmed.html",
+    resources:
+        mem_mb=10000 if get_max_mb(0.5) > 10000 else get_max_mb(0.5),
     params:
         "--quiet",
     wildcard_constraints:
@@ -151,6 +155,8 @@ rule fastqc_merged:  # qc on trimmed, merged reads
     output:
         zip="output/qc/fastqc/{sample}-{read}-merged_fastqc.zip",
         html="output/qc/fastqc/{sample}-{read}-merged.html",
+    resources:
+        mem_mb=10000 if get_max_mb(0.5) > 10000 else get_max_mb(0.5),
     params:
         "--quiet",
     wildcard_constraints:

From 05ecaf222ce05e0ef0e0b785090bdf2232d8b371 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 5 Mar 2024 12:42:50 +1100
Subject: [PATCH 5/7] Fix function 'get_prokka_output'

---
 metaphor/workflow/rules/common.smk | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/metaphor/workflow/rules/common.smk b/metaphor/workflow/rules/common.smk
index a3a287e..2285c11 100644
--- a/metaphor/workflow/rules/common.smk
+++ b/metaphor/workflow/rules/common.smk
@@ -496,7 +496,7 @@ def get_prokka_output():
     bins_dict = {}
     for group in binning_group_names:
         bins_dict[group] = glob(
-            f"output/binning/DAS_tool/{group}/DAS_tool_DASTool_bins/*"
+            f"output/binning/DAS_tool/{group}/{group}_DASTool_bins/*"
         )
 
     for group, list_of_bins in bins_dict.items():

From fb692802f4f91bf1b1be76f343df12ec5de6e9ba Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 5 Mar 2024 12:52:08 +1100
Subject: [PATCH 6/7] Improve for rule 'prokka'

---
 metaphor/workflow/rules/annotation.smk | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/metaphor/workflow/rules/annotation.smk b/metaphor/workflow/rules/annotation.smk
index 749daa0..4e412fc 100644
--- a/metaphor/workflow/rules/annotation.smk
+++ b/metaphor/workflow/rules/annotation.smk
@@ -78,7 +78,6 @@ rule prokka:
         outfile="output/annotation/prokka/{binning_group}/{bin}/{bin}.fna",
     params:
         outdir=lambda w, output: str(Path(output.outfile).parent),
-        kingdom_cmd=lambda w, input: f"grep '{w.bin}' {input.bin_evals}",
         args=config["prokka"]["args"],
     wildcard_constraints:
         binning_group="|".join(binning_group_names),
@@ -94,7 +93,8 @@ rule prokka:
     shell:
         """
         # Get kingdom from bin eval file
-        kingdom=$({params.kingdom_cmd} | cut -f 5)
+        bin_clean=$(echo {wildcards.bin} | sed 's/_sub$//g')  # Remove '_sub' from corrected bins
+        kingdom=$(grep $bin_clean {input.bin_evals} | cut -f 5)
         kingdom=$(echo $kingdom | head -c 1 | tr '[a-z]' '[A-Z]'; echo $kingdom | tail -c +2)
 
         prokka --outdir {params.outdir}     \

From 2fce82e81a8c30c40df59a95d8d87f9df68c1333 Mon Sep 17 00:00:00 2001
From: Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Date: Tue, 5 Mar 2024 13:28:57 +1100
Subject: [PATCH 7/7] Further improve Prokka command

---
 metaphor/workflow/rules/annotation.smk | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/metaphor/workflow/rules/annotation.smk b/metaphor/workflow/rules/annotation.smk
index 4e412fc..ca53811 100644
--- a/metaphor/workflow/rules/annotation.smk
+++ b/metaphor/workflow/rules/annotation.smk
@@ -78,7 +78,7 @@ rule prokka:
         outfile="output/annotation/prokka/{binning_group}/{bin}/{bin}.fna",
     params:
         outdir=lambda w, output: str(Path(output.outfile).parent),
-        args=config["prokka"]["args"],
+        args=config["prokka"]["args"] + " --centre X --compliant",
     wildcard_constraints:
         binning_group="|".join(binning_group_names),
     threads: get_threads_per_task_size("small")
@@ -95,6 +95,7 @@ rule prokka:
         # Get kingdom from bin eval file
         bin_clean=$(echo {wildcards.bin} | sed 's/_sub$//g')  # Remove '_sub' from corrected bins
         kingdom=$(grep $bin_clean {input.bin_evals} | cut -f 5)
+        kingdom=$(echo $kingdom | cut -f 1 -d ' ')
         kingdom=$(echo $kingdom | head -c 1 | tr '[a-z]' '[A-Z]'; echo $kingdom | tail -c +2)
 
         prokka --outdir {params.outdir}     \