From f46ec833ed56c39820c0a0e8d8e0295050a334ab Mon Sep 17 00:00:00 2001
From: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Date: Tue, 20 Aug 2024 13:58:39 +0200
Subject: [PATCH 1/7] fix: pangolin data updates (#662)

* restructure data download

* fmt

* change name

* change name of rule

* remove old rules

* change input name
---
 workflow/rules/ref.smk            | 27 +++++----------------------
 workflow/rules/strain_calling.smk |  7 ++-----
 2 files changed, 7 insertions(+), 27 deletions(-)

diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
index 6c0131c8..31fa8502 100644
--- a/workflow/rules/ref.smk
+++ b/workflow/rules/ref.smk
@@ -191,32 +191,15 @@ rule get_human_genome:
         "curl -SL -o {output} {params.human_genome} 2> {log}"
 
 
-rule update_pangoLEARN:
+rule get_pangolin_data:
     output:
-        directory("results/{date}/pangolin/pangoLEARN"),
+        "results/{date}/pangolin/pangolin-data.log",
     log:
-        "logs/{date}/pangolin/update.log",
+        "logs/{date}/pangolin/pangolin-data.log",
     conda:
-        "../envs/unix.yaml"
-    shell:
-        "(mkdir -p {output} &&"
-        " curl -L https://github.com/cov-lineages/pangoLEARN/archive/master.tar.gz |"
-        " tar xvz --strip-components=1 -C {output})"
-        " > {log} 2>&1"
-
-
-rule update_lineages:
-    output:
-        directory("results/{date}/pangolin/lineages"),
-    log:
-        "logs/{date}/pangolin/update.log",
-    conda:
-        "../envs/unix.yaml"
+        "../envs/pangolin.yaml"
     shell:
-        "(mkdir -p {output} &&"
-        " curl -L https://github.com/cov-lineages/lineages/archive/master.tar.gz | "
-        " tar xvz --strip-components=1 -C {output})"
-        " > {log} 2>&1"
+        "pangolin --update-data > {log} 2>&1 && cp {log} {output}"
 
 
 rule get_gisaid_provision:
diff --git a/workflow/rules/strain_calling.smk b/workflow/rules/strain_calling.smk
index 0d86db0a..88d8a603 100644
--- a/workflow/rules/strain_calling.smk
+++ b/workflow/rules/strain_calling.smk
@@ -141,19 +141,16 @@ rule kallisto_plot_all_strains:
 rule pangolin_call_strains:
     input:
         contigs=get_pangolin_input,
-        pangoLEARN="results/{date}/pangolin/pangoLEARN",
-        lineages="results/{date}/pangolin/lineages",
+        data="results/{date}/pangolin/pangolin-data.log",
     output:
         "results/{date}/tables/strain-calls/{sample}.{stage}.strains.pangolin.csv",
     log:
         "logs/{date}/pangolin/{sample}.{stage}.log",
-    params:
-        pango_data_path=lambda w, input: os.path.dirname(input.pangoLEARN),
     conda:
         "../envs/pangolin.yaml"
     threads: 8
     shell:
-        "pangolin {input.contigs} --data {params.pango_data_path} --outfile {output} > {log} 2>&1"
+        "pangolin {input.contigs} --outfile {output} > {log} 2>&1"
 
 
 rule pangolin_plot_all_strains:

From f77d42e2154a95b6ca0e2c127df8ca134eda1789 Mon Sep 17 00:00:00 2001
From: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Date: Thu, 29 Aug 2024 12:18:01 +0200
Subject: [PATCH 2/7] feat: FLiRT Mutations column (#664)

* init

* fmt

* add to other config.yaml and template files

* add def

* add to env output

* fmt
---
 .tests/config/config.yaml                   |  6 +++++
 config/config.yaml                          | 14 +++++++----
 resources/report-table-formatter.js         |  3 +++
 workflow/rules/generate_output.smk          | 26 +++++++++++++--------
 workflow/schemas/config.schema.yaml         |  4 ++++
 workflow/scripts/generate-overview-table.py |  6 ++++-
 6 files changed, 44 insertions(+), 15 deletions(-)

diff --git a/.tests/config/config.yaml b/.tests/config/config.yaml
index 25a8ea6f..5a278a36 100644
--- a/.tests/config/config.yaml
+++ b/.tests/config/config.yaml
@@ -166,6 +166,12 @@ mixtures:
     - "_MIX_B-1-1-7_PERC_90_MIX_B-1-351_PERC_10"
 
 # mutations to be highlighted (protein name -> variants)
+
+flirt:
+  S:
+    - F456L
+    - R346T
+
 mth:
   S:
     - N501Y
diff --git a/config/config.yaml b/config/config.yaml
index 898b305a..84b0886f 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -21,7 +21,7 @@ data-handling:
   # flag for archiving data
   # True: data is archived in path defined below
   # False: data is not archived
-  archive-data: True
+  archive-data: False
   # path of incoming data, which is moved to the
   # data directory by the preprocessing script
   incoming: ../incoming/
@@ -34,7 +34,7 @@ data-handling:
 quality-criteria:
   illumina:
     # minimal length of acceptable reads
-    min-length-reads: 30
+    min-length-reads: 100
     # average quality of acceptable reads (PHRED)
     min-PHRED: 20
   ont:
@@ -61,9 +61,9 @@ preprocessing:
   # ARTIC primer version to clip from reads. See
   # https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V4
   # for more information
-  artic-primer-version: 3
+  artic-primer-version: 4
   # path to amplicon primers in bed format for hard-clipping on paired end files (illumina) or url to file that should be downloaded
-  amplicon-primers: "resources/nCoV-2019.primer.bed"
+  amplicon-primers: "resources/SARS-CoV-2-artic-v4_1.primer.bed"
   # GenBank accession of reference sequence of the amplicon primers
   amplicon-reference: "MN908947"
 
@@ -124,6 +124,12 @@ strain-calling:
     B.1.617.2: OK091006
 
 # mutations to be highlighted (protein name -> variants)
+
+flirt:
+  S:
+    - F456L
+    - R346T
+
 mth:
   S:
     - L18F
diff --git a/resources/report-table-formatter.js b/resources/report-table-formatter.js
index ab07f158..c2d1a13d 100644
--- a/resources/report-table-formatter.js
+++ b/resources/report-table-formatter.js
@@ -91,6 +91,9 @@
       }
 
   },
+  "FLiRT Mutations": function format(value) {
+    return this["variant helper"](value, true);
+  },
   "VOC Mutations": function format(value) {
       return this["variant helper"](value, true);
   },
diff --git a/workflow/rules/generate_output.smk b/workflow/rules/generate_output.smk
index 11899c10..c272e783 100644
--- a/workflow/rules/generate_output.smk
+++ b/workflow/rules/generate_output.smk
@@ -153,6 +153,7 @@ rule overview_table_patient_csv:
             wildcards, "all samples"
         ),
         mth=config.get("mth"),
+        flirt=config.get("flirt"),
         samples=lambda wildcards: get_samples_for_date(wildcards.date),
         mode=config["mode"],
     log:
@@ -178,6 +179,7 @@ use rule overview_table_patient_csv as overview_table_environment_csv with:
         qc_data="results/{date}/tables/environment-overview.csv",
     params:
         mth=config.get("mth"),
+        flirt=config.get("flirt"),
         samples=lambda wildcards: get_samples_for_date(wildcards.date),
         mode=config["mode"],
     log:
@@ -371,6 +373,7 @@ rule snakemake_reports_patient:
         expand_samples_for_date(
             ["results/{{date}}/lineage-variant-report/{sample}.lineage-variants"]
         ),
+        # lambda wildcards: "results/{date}/lineage-variant-report/all",
         lambda wildcards: expand(
             "results/{{date}}/vcf-report/{target}.{filter}.{annotation}",
             target=get_samples_for_date(wildcards.date) + ["all"],
@@ -380,10 +383,10 @@ rule snakemake_reports_patient:
         # 3. Sequencing Details
         "results/{date}/qc/laboratory/multiqc.html",
         "results/{date}/plots/coverage-reference-genome.png",
-        "results/{date}/plots/coverage-assembled-genome.png",
-        lambda wildcards: "results/{date}/plots/primer-clipping-intervals.svg"
-        if any_sample_is_amplicon(wildcards)
-        else [],
+        # "results/{date}/plots/coverage-assembled-genome.png",
+        # lambda wildcards: "results/{date}/plots/primer-clipping-intervals.svg"
+        # if any_sample_is_amplicon(wildcards)
+        # else [],
         # 4. Assembly
         "results/{date}/filter-overview",
         "results/{date}/pangolin-call-overview",
@@ -406,8 +409,6 @@ rule snakemake_reports_patient:
         "results/patient-reports/{date}.zip",
     params:
         for_testing=get_if_testing("--snakefile ../workflow/Snakefile"),
-    conda:
-        "../envs/snakemake.yaml"
     log:
         "logs/snakemake_reports/{date}.log",
     shell:
@@ -423,10 +424,10 @@ use rule snakemake_reports_patient as snakemake_reports_environment with:
             "results/{{date}}/{execution_mode}/overview/",
             execution_mode=get_checked_mode(),
         ),
-        "results/{date}/plots/all.major-strain.strains.kallisto.svg",
-        expand_samples_for_date(
-            ["results/{{date}}/plots/strain-calls/{sample}.strains.kallisto.svg"]
-        ),
+        # "results/{date}/plots/all.major-strain.strains.kallisto.svg",
+        # expand_samples_for_date(
+        #     ["results/{{date}}/plots/strain-calls/{sample}.strains.kallisto.svg"]
+        # ),
         # 2. Variant Call Details
         expand_samples_for_date(
             ["results/{{date}}/lineage-variant-report/{sample}.lineage-variants"]
@@ -444,3 +445,8 @@ use rule snakemake_reports_patient as snakemake_reports_environment with:
         "results/environment-reports/{date}.zip",
     log:
         "logs/snakemake_reports/{date}.log",
+
+
+# rule output_sample_sheet:
+#     input:
+#         Path(pep.config_file()).parent / pep.config()["sample_table"],
diff --git a/workflow/schemas/config.schema.yaml b/workflow/schemas/config.schema.yaml
index d4d49881..2ae788b7 100644
--- a/workflow/schemas/config.schema.yaml
+++ b/workflow/schemas/config.schema.yaml
@@ -115,6 +115,9 @@ properties:
         description: flag for using gisaid or genbank
       lineage-references:
         type: object
+  flirt:
+    type: object
+    description: mutations to be highlighted (protein name -> variants)
   mth:
     type: object
     description: mutations to be highlighted (protein name -> variants)
@@ -130,4 +133,5 @@ required:
   - assembly
   - variant-calling
   - strain-calling
+  - flirt
   - mth
diff --git a/workflow/scripts/generate-overview-table.py b/workflow/scripts/generate-overview-table.py
index 9afd487b..aebe14c6 100644
--- a/workflow/scripts/generate-overview-table.py
+++ b/workflow/scripts/generate-overview-table.py
@@ -193,6 +193,7 @@ def register_contig_lengths(assemblies, name):
 }
 
 for sample, file in iter_with_samples(snakemake.input.bcf):
+    flirt_mutations = {}
     mutations_of_interest = {}
     other_mutations = {}
 
@@ -228,11 +229,14 @@ def fmt_variants(variants):
 
                     hgvsp = f"{feature}:{alteration}"
                     entry = (hgvsp, f"{vaf:.3f}")
-                    if alteration in snakemake.params.mth.get(feature, {}):
+                    if alteration in snakemake.params.flirt.get(feature, {}):
+                        insert_entry(flirt_mutations, hgvsp, vaf)
+                    elif alteration in snakemake.params.mth.get(feature, {}):
                         insert_entry(mutations_of_interest, hgvsp, vaf)
                     else:
                         insert_entry(other_mutations, hgvsp, vaf)
 
+    data.loc[sample, "FLiRT Mutations"] = fmt_variants(flirt_mutations)
     data.loc[sample, "VOC Mutations"] = fmt_variants(mutations_of_interest)
     data.loc[sample, "Other Mutations"] = fmt_variants(other_mutations)
 

From 5c5a108acbb8131c1f036ba6ba4eb3b9a7433205 Mon Sep 17 00:00:00 2001
From: vBassewitz <104062464+vBassewitz@users.noreply.github.com>
Date: Wed, 11 Sep 2024 17:22:22 +0200
Subject: [PATCH 3/7] Revert "feat: FLiRT Mutations column (#664)" (#667)

This reverts commit f77d42e2154a95b6ca0e2c127df8ca134eda1789.
---
 .tests/config/config.yaml                   |  6 -----
 config/config.yaml                          | 14 ++++-------
 resources/report-table-formatter.js         |  3 ---
 workflow/rules/generate_output.smk          | 26 ++++++++-------------
 workflow/schemas/config.schema.yaml         |  4 ----
 workflow/scripts/generate-overview-table.py |  6 +----
 6 files changed, 15 insertions(+), 44 deletions(-)

diff --git a/.tests/config/config.yaml b/.tests/config/config.yaml
index 5a278a36..25a8ea6f 100644
--- a/.tests/config/config.yaml
+++ b/.tests/config/config.yaml
@@ -166,12 +166,6 @@ mixtures:
     - "_MIX_B-1-1-7_PERC_90_MIX_B-1-351_PERC_10"
 
 # mutations to be highlighted (protein name -> variants)
-
-flirt:
-  S:
-    - F456L
-    - R346T
-
 mth:
   S:
     - N501Y
diff --git a/config/config.yaml b/config/config.yaml
index 84b0886f..898b305a 100644
--- a/config/config.yaml
+++ b/config/config.yaml
@@ -21,7 +21,7 @@ data-handling:
   # flag for archiving data
   # True: data is archived in path defined below
   # False: data is not archived
-  archive-data: False
+  archive-data: True
   # path of incoming data, which is moved to the
   # data directory by the preprocessing script
   incoming: ../incoming/
@@ -34,7 +34,7 @@ data-handling:
 quality-criteria:
   illumina:
     # minimal length of acceptable reads
-    min-length-reads: 100
+    min-length-reads: 30
     # average quality of acceptable reads (PHRED)
     min-PHRED: 20
   ont:
@@ -61,9 +61,9 @@ preprocessing:
   # ARTIC primer version to clip from reads. See
   # https://github.com/artic-network/artic-ncov2019/tree/master/primer_schemes/nCoV-2019/V4
   # for more information
-  artic-primer-version: 4
+  artic-primer-version: 3
   # path to amplicon primers in bed format for hard-clipping on paired end files (illumina) or url to file that should be downloaded
-  amplicon-primers: "resources/SARS-CoV-2-artic-v4_1.primer.bed"
+  amplicon-primers: "resources/nCoV-2019.primer.bed"
   # GenBank accession of reference sequence of the amplicon primers
   amplicon-reference: "MN908947"
 
@@ -124,12 +124,6 @@ strain-calling:
     B.1.617.2: OK091006
 
 # mutations to be highlighted (protein name -> variants)
-
-flirt:
-  S:
-    - F456L
-    - R346T
-
 mth:
   S:
     - L18F
diff --git a/resources/report-table-formatter.js b/resources/report-table-formatter.js
index c2d1a13d..ab07f158 100644
--- a/resources/report-table-formatter.js
+++ b/resources/report-table-formatter.js
@@ -91,9 +91,6 @@
       }
 
   },
-  "FLiRT Mutations": function format(value) {
-    return this["variant helper"](value, true);
-  },
   "VOC Mutations": function format(value) {
       return this["variant helper"](value, true);
   },
diff --git a/workflow/rules/generate_output.smk b/workflow/rules/generate_output.smk
index c272e783..11899c10 100644
--- a/workflow/rules/generate_output.smk
+++ b/workflow/rules/generate_output.smk
@@ -153,7 +153,6 @@ rule overview_table_patient_csv:
             wildcards, "all samples"
         ),
         mth=config.get("mth"),
-        flirt=config.get("flirt"),
         samples=lambda wildcards: get_samples_for_date(wildcards.date),
         mode=config["mode"],
     log:
@@ -179,7 +178,6 @@ use rule overview_table_patient_csv as overview_table_environment_csv with:
         qc_data="results/{date}/tables/environment-overview.csv",
     params:
         mth=config.get("mth"),
-        flirt=config.get("flirt"),
         samples=lambda wildcards: get_samples_for_date(wildcards.date),
         mode=config["mode"],
     log:
@@ -373,7 +371,6 @@ rule snakemake_reports_patient:
         expand_samples_for_date(
             ["results/{{date}}/lineage-variant-report/{sample}.lineage-variants"]
         ),
-        # lambda wildcards: "results/{date}/lineage-variant-report/all",
         lambda wildcards: expand(
             "results/{{date}}/vcf-report/{target}.{filter}.{annotation}",
             target=get_samples_for_date(wildcards.date) + ["all"],
@@ -383,10 +380,10 @@ rule snakemake_reports_patient:
         # 3. Sequencing Details
         "results/{date}/qc/laboratory/multiqc.html",
         "results/{date}/plots/coverage-reference-genome.png",
-        # "results/{date}/plots/coverage-assembled-genome.png",
-        # lambda wildcards: "results/{date}/plots/primer-clipping-intervals.svg"
-        # if any_sample_is_amplicon(wildcards)
-        # else [],
+        "results/{date}/plots/coverage-assembled-genome.png",
+        lambda wildcards: "results/{date}/plots/primer-clipping-intervals.svg"
+        if any_sample_is_amplicon(wildcards)
+        else [],
         # 4. Assembly
         "results/{date}/filter-overview",
         "results/{date}/pangolin-call-overview",
@@ -409,6 +406,8 @@ rule snakemake_reports_patient:
         "results/patient-reports/{date}.zip",
     params:
         for_testing=get_if_testing("--snakefile ../workflow/Snakefile"),
+    conda:
+        "../envs/snakemake.yaml"
     log:
         "logs/snakemake_reports/{date}.log",
     shell:
@@ -424,10 +423,10 @@ use rule snakemake_reports_patient as snakemake_reports_environment with:
             "results/{{date}}/{execution_mode}/overview/",
             execution_mode=get_checked_mode(),
         ),
-        # "results/{date}/plots/all.major-strain.strains.kallisto.svg",
-        # expand_samples_for_date(
-        #     ["results/{{date}}/plots/strain-calls/{sample}.strains.kallisto.svg"]
-        # ),
+        "results/{date}/plots/all.major-strain.strains.kallisto.svg",
+        expand_samples_for_date(
+            ["results/{{date}}/plots/strain-calls/{sample}.strains.kallisto.svg"]
+        ),
         # 2. Variant Call Details
         expand_samples_for_date(
             ["results/{{date}}/lineage-variant-report/{sample}.lineage-variants"]
@@ -445,8 +444,3 @@ use rule snakemake_reports_patient as snakemake_reports_environment with:
         "results/environment-reports/{date}.zip",
     log:
         "logs/snakemake_reports/{date}.log",
-
-
-# rule output_sample_sheet:
-#     input:
-#         Path(pep.config_file()).parent / pep.config()["sample_table"],
diff --git a/workflow/schemas/config.schema.yaml b/workflow/schemas/config.schema.yaml
index 2ae788b7..d4d49881 100644
--- a/workflow/schemas/config.schema.yaml
+++ b/workflow/schemas/config.schema.yaml
@@ -115,9 +115,6 @@ properties:
         description: flag for using gisaid or genbank
       lineage-references:
         type: object
-  flirt:
-    type: object
-    description: mutations to be highlighted (protein name -> variants)
   mth:
     type: object
     description: mutations to be highlighted (protein name -> variants)
@@ -133,5 +130,4 @@ required:
   - assembly
   - variant-calling
   - strain-calling
-  - flirt
   - mth
diff --git a/workflow/scripts/generate-overview-table.py b/workflow/scripts/generate-overview-table.py
index aebe14c6..9afd487b 100644
--- a/workflow/scripts/generate-overview-table.py
+++ b/workflow/scripts/generate-overview-table.py
@@ -193,7 +193,6 @@ def register_contig_lengths(assemblies, name):
 }
 
 for sample, file in iter_with_samples(snakemake.input.bcf):
-    flirt_mutations = {}
     mutations_of_interest = {}
     other_mutations = {}
 
@@ -229,14 +228,11 @@ def fmt_variants(variants):
 
                     hgvsp = f"{feature}:{alteration}"
                     entry = (hgvsp, f"{vaf:.3f}")
-                    if alteration in snakemake.params.flirt.get(feature, {}):
-                        insert_entry(flirt_mutations, hgvsp, vaf)
-                    elif alteration in snakemake.params.mth.get(feature, {}):
+                    if alteration in snakemake.params.mth.get(feature, {}):
                         insert_entry(mutations_of_interest, hgvsp, vaf)
                     else:
                         insert_entry(other_mutations, hgvsp, vaf)
 
-    data.loc[sample, "FLiRT Mutations"] = fmt_variants(flirt_mutations)
     data.loc[sample, "VOC Mutations"] = fmt_variants(mutations_of_interest)
     data.loc[sample, "Other Mutations"] = fmt_variants(other_mutations)
 

From b8c5c449f81ba9c08bcdb68a099318eca1e64066 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@tu-dortmund.de>
Date: Thu, 17 Oct 2024 18:31:12 +0200
Subject: [PATCH 4/7] chore: checkout full history for formatting (#668)

* chore: checkout full history for formatting

* force latest pangolin

* work around pangolin dependency issues

* Update spades.yaml

---------

Co-authored-by: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
Co-authored-by: Alex Thomas <alex.thomas89@gmail.com>
---
 .github/workflows/main.yml  | 2 ++
 workflow/envs/pangolin.yaml | 1 +
 workflow/envs/spades.yaml   | 2 +-
 3 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 51391772..fe93b6a9 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -23,6 +23,8 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
+        with:
+          depth: 0
       - name: Formatting
         uses: super-linter/super-linter@v5.7.2
         env:
diff --git a/workflow/envs/pangolin.yaml b/workflow/envs/pangolin.yaml
index f6a26ad4..42265aca 100644
--- a/workflow/envs/pangolin.yaml
+++ b/workflow/envs/pangolin.yaml
@@ -4,3 +4,4 @@ channels:
   - nodefaults
 dependencies:
   - pangolin =4.3
+  - snakemake-minimal=7.24.0 # TODO keep until https://github.com/bioconda/bioconda-recipes/pull/42192 and we can pin to 4.3.1 above
diff --git a/workflow/envs/spades.yaml b/workflow/envs/spades.yaml
index d88fde2c..32c7a4d3 100644
--- a/workflow/envs/spades.yaml
+++ b/workflow/envs/spades.yaml
@@ -3,4 +3,4 @@ channels:
   - bioconda
   - nodefaults
 dependencies:
-  - spades =3.15
+  - spades =4.0

From 576329c0b82ebe5784fb5cdd845f77ee8834a84d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 18 Oct 2024 08:46:51 +0200
Subject: [PATCH 5/7] chore(deps): bump peter-evans/create-pull-request from 6
 to 7 (#666)

Bumps [peter-evans/create-pull-request](https://github.com/peter-evans/create-pull-request) from 6 to 7.
- [Release notes](https://github.com/peter-evans/create-pull-request/releases)
- [Commits](https://github.com/peter-evans/create-pull-request/compare/v6...v7)

---
updated-dependencies:
- dependency-name: peter-evans/create-pull-request
  dependency-type: direct:production
  update-type: version-update:semver-major
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: Alexander Thomas <77535027+alethomas@users.noreply.github.com>
---
 .github/workflows/copyright-preamble.yml | 2 +-
 .github/workflows/update-pangolin.yaml   | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/copyright-preamble.yml b/.github/workflows/copyright-preamble.yml
index dbf88af6..81d5f573 100644
--- a/.github/workflows/copyright-preamble.yml
+++ b/.github/workflows/copyright-preamble.yml
@@ -25,7 +25,7 @@ jobs:
 
       # Creates pull request with all changes in file
       - name: Create Pull Request
-        uses: peter-evans/create-pull-request@v6
+        uses: peter-evans/create-pull-request@v7
         with:
           commit-message: "chore: update copyright preamble"
           delete-branch: true
diff --git a/.github/workflows/update-pangolin.yaml b/.github/workflows/update-pangolin.yaml
index 1945cc86..7e7021c0 100644
--- a/.github/workflows/update-pangolin.yaml
+++ b/.github/workflows/update-pangolin.yaml
@@ -37,7 +37,7 @@ jobs:
       - name: Create Pull Request
         if: ${{ env.LATEST_PANGOLIN != env.CURRENT_PANGOLIN }}
         id: cpr
-        uses: peter-evans/create-pull-request@v6
+        uses: peter-evans/create-pull-request@v7
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           committer: GitHub <noreply@github.com>

From 9cb1576a8c41c23344940f2248e5d44464a53b2e Mon Sep 17 00:00:00 2001
From: Hamdiye Uzuner <hamdiyeuzuner@gmail.com>
Date: Wed, 23 Oct 2024 14:00:37 +0200
Subject: [PATCH 6/7] fix: move primer file location under workflow; this
 avoids file not being found in shared filesystems (#665)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* fix: move nCoV-2019.primer.bed under workflow/resources

* fix: fix path of primers in main config

* fix: fix primer path to be called internally

* fix: fix same in previous commit in read_clipping.smk

* define a function for getting kracken input in common.smk

* fix get_kracken_input()

* use get_kracken_input in qc.smk

* restore all changes

* refactor: move checking the primer file for URL into the script

* chore: fmt

* fix: disable formatting temporarily

* Update main.yml

* Update main.yml

* fmt script

* add missing key to artifact name

---------

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
---
 .github/workflows/main.yml              |   6 +-
 workflow/resources/nCoV-2019.primer.bed | 218 ++++++++++++++++++++++++
 workflow/rules/common.smk               |  32 ++--
 workflow/rules/generate_output.smk      |   8 +-
 workflow/rules/read_clipping.smk        |   2 +-
 workflow/rules/ref.smk                  |   8 +-
 workflow/rules/variant_calling.smk      |   8 +-
 workflow/scripts/bed-to-bedpe.py        |  18 +-
 8 files changed, 273 insertions(+), 27 deletions(-)
 create mode 100644 workflow/resources/nCoV-2019.primer.bed

diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index fe93b6a9..b2a96028 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -24,7 +24,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          depth: 0
+          fetch-depth: 0
       - name: Formatting
         uses: super-linter/super-linter@v5.7.2
         env:
@@ -66,7 +66,6 @@ jobs:
     env:
       GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }}
     needs:
-      - Formatting
       - Linting
       #- Pre-Commit
     strategy:
@@ -181,7 +180,7 @@ jobs:
         uses: actions/upload-artifact@v4
         if: matrix.technology == 'all' && matrix.rule != 'all -npr'
         with:
-          name: log-rule-${{ matrix.rule }}-technology-${{ matrix.technology }}
+          name: log-rule-${{ matrix.rule }}-technology-${{ matrix.technology }}-${{ matrix.seq_method }}
           path: .tests/logs/
 
       - name: Change permissions for caching
@@ -195,7 +194,6 @@ jobs:
     env:
       GISAID_API_TOKEN: ${{ secrets.GISAID_API_TOKEN }}
     needs:
-      - Formatting
       - Linting
       #- Pre-Commit
     strategy:
diff --git a/workflow/resources/nCoV-2019.primer.bed b/workflow/resources/nCoV-2019.primer.bed
new file mode 100644
index 00000000..76691de9
--- /dev/null
+++ b/workflow/resources/nCoV-2019.primer.bed
@@ -0,0 +1,218 @@
+MN908947.3	30	54	nCoV-2019_1_LEFT	1	+
+MN908947.3	385	410	nCoV-2019_1_RIGHT	1	-
+MN908947.3	320	342	nCoV-2019_2_LEFT	2	+
+MN908947.3	704	726	nCoV-2019_2_RIGHT	2	-
+MN908947.3	642	664	nCoV-2019_3_LEFT	1	+
+MN908947.3	1004	1028	nCoV-2019_3_RIGHT	1	-
+MN908947.3	943	965	nCoV-2019_4_LEFT	2	+
+MN908947.3	1312	1337	nCoV-2019_4_RIGHT	2	-
+MN908947.3	1242	1264	nCoV-2019_5_LEFT	1	+
+MN908947.3	1623	1651	nCoV-2019_5_RIGHT	1	-
+MN908947.3	1573	1595	nCoV-2019_6_LEFT	2	+
+MN908947.3	1942	1964	nCoV-2019_6_RIGHT	2	-
+MN908947.3	1875	1897	nCoV-2019_7_LEFT	1	+
+MN908947.3	1868	1890	nCoV-2019_7_LEFT_alt0	1	+
+MN908947.3	2247	2269	nCoV-2019_7_RIGHT	1	-
+MN908947.3	2242	2264	nCoV-2019_7_RIGHT_alt5	1	-
+MN908947.3	2181	2205	nCoV-2019_8_LEFT	2	+
+MN908947.3	2568	2592	nCoV-2019_8_RIGHT	2	-
+MN908947.3	2505	2529	nCoV-2019_9_LEFT	1	+
+MN908947.3	2504	2528	nCoV-2019_9_LEFT_alt4	1	+
+MN908947.3	2882	2904	nCoV-2019_9_RIGHT	1	-
+MN908947.3	2880	2902	nCoV-2019_9_RIGHT_alt2	1	-
+MN908947.3	2826	2850	nCoV-2019_10_LEFT	2	+
+MN908947.3	3183	3210	nCoV-2019_10_RIGHT	2	-
+MN908947.3	3144	3166	nCoV-2019_11_LEFT	1	+
+MN908947.3	3507	3531	nCoV-2019_11_RIGHT	1	-
+MN908947.3	3460	3482	nCoV-2019_12_LEFT	2	+
+MN908947.3	3826	3853	nCoV-2019_12_RIGHT	2	-
+MN908947.3	3771	3795	nCoV-2019_13_LEFT	1	+
+MN908947.3	4142	4164	nCoV-2019_13_RIGHT	1	-
+MN908947.3	4054	4077	nCoV-2019_14_LEFT	2	+
+MN908947.3	4044	4068	nCoV-2019_14_LEFT_alt4	2	+
+MN908947.3	4428	4450	nCoV-2019_14_RIGHT	2	-
+MN908947.3	4402	4424	nCoV-2019_14_RIGHT_alt2	2	-
+MN908947.3	4294	4321	nCoV-2019_15_LEFT	1	+
+MN908947.3	4296	4322	nCoV-2019_15_LEFT_alt1	1	+
+MN908947.3	4674	4696	nCoV-2019_15_RIGHT	1	-
+MN908947.3	4666	4689	nCoV-2019_15_RIGHT_alt3	1	-
+MN908947.3	4636	4658	nCoV-2019_16_LEFT	2	+
+MN908947.3	4995	5017	nCoV-2019_16_RIGHT	2	-
+MN908947.3	4939	4966	nCoV-2019_17_LEFT	1	+
+MN908947.3	5296	5321	nCoV-2019_17_RIGHT	1	-
+MN908947.3	5230	5259	nCoV-2019_18_LEFT	2	+
+MN908947.3	5257	5287	nCoV-2019_18_LEFT_alt2	2	+
+MN908947.3	5620	5644	nCoV-2019_18_RIGHT	2	-
+MN908947.3	5620	5643	nCoV-2019_18_RIGHT_alt1	2	-
+MN908947.3	5563	5586	nCoV-2019_19_LEFT	1	+
+MN908947.3	5932	5957	nCoV-2019_19_RIGHT	1	-
+MN908947.3	5867	5894	nCoV-2019_20_LEFT	2	+
+MN908947.3	6247	6272	nCoV-2019_20_RIGHT	2	-
+MN908947.3	6167	6196	nCoV-2019_21_LEFT	1	+
+MN908947.3	6168	6197	nCoV-2019_21_LEFT_alt2	1	+
+MN908947.3	6528	6550	nCoV-2019_21_RIGHT	1	-
+MN908947.3	6526	6548	nCoV-2019_21_RIGHT_alt0	1	-
+MN908947.3	6466	6495	nCoV-2019_22_LEFT	2	+
+MN908947.3	6846	6873	nCoV-2019_22_RIGHT	2	-
+MN908947.3	6718	6745	nCoV-2019_23_LEFT	1	+
+MN908947.3	7092	7117	nCoV-2019_23_RIGHT	1	-
+MN908947.3	7035	7058	nCoV-2019_24_LEFT	2	+
+MN908947.3	7389	7415	nCoV-2019_24_RIGHT	2	-
+MN908947.3	7305	7332	nCoV-2019_25_LEFT	1	+
+MN908947.3	7671	7694	nCoV-2019_25_RIGHT	1	-
+MN908947.3	7626	7651	nCoV-2019_26_LEFT	2	+
+MN908947.3	7997	8019	nCoV-2019_26_RIGHT	2	-
+MN908947.3	7943	7968	nCoV-2019_27_LEFT	1	+
+MN908947.3	8319	8341	nCoV-2019_27_RIGHT	1	-
+MN908947.3	8249	8275	nCoV-2019_28_LEFT	2	+
+MN908947.3	8635	8661	nCoV-2019_28_RIGHT	2	-
+MN908947.3	8595	8619	nCoV-2019_29_LEFT	1	+
+MN908947.3	8954	8983	nCoV-2019_29_RIGHT	1	-
+MN908947.3	8888	8913	nCoV-2019_30_LEFT	2	+
+MN908947.3	9245	9271	nCoV-2019_30_RIGHT	2	-
+MN908947.3	9204	9226	nCoV-2019_31_LEFT	1	+
+MN908947.3	9557	9585	nCoV-2019_31_RIGHT	1	-
+MN908947.3	9477	9502	nCoV-2019_32_LEFT	2	+
+MN908947.3	9834	9858	nCoV-2019_32_RIGHT	2	-
+MN908947.3	9784	9806	nCoV-2019_33_LEFT	1	+
+MN908947.3	10146	10171	nCoV-2019_33_RIGHT	1	-
+MN908947.3	10076	10099	nCoV-2019_34_LEFT	2	+
+MN908947.3	10437	10459	nCoV-2019_34_RIGHT	2	-
+MN908947.3	10362	10384	nCoV-2019_35_LEFT	1	+
+MN908947.3	10737	10763	nCoV-2019_35_RIGHT	1	-
+MN908947.3	10666	10688	nCoV-2019_36_LEFT	2	+
+MN908947.3	11048	11074	nCoV-2019_36_RIGHT	2	-
+MN908947.3	10999	11022	nCoV-2019_37_LEFT	1	+
+MN908947.3	11372	11394	nCoV-2019_37_RIGHT	1	-
+MN908947.3	11306	11331	nCoV-2019_38_LEFT	2	+
+MN908947.3	11668	11693	nCoV-2019_38_RIGHT	2	-
+MN908947.3	11555	11584	nCoV-2019_39_LEFT	1	+
+MN908947.3	11927	11949	nCoV-2019_39_RIGHT	1	-
+MN908947.3	11863	11889	nCoV-2019_40_LEFT	2	+
+MN908947.3	12234	12256	nCoV-2019_40_RIGHT	2	-
+MN908947.3	12110	12133	nCoV-2019_41_LEFT	1	+
+MN908947.3	12465	12490	nCoV-2019_41_RIGHT	1	-
+MN908947.3	12417	12439	nCoV-2019_42_LEFT	2	+
+MN908947.3	12779	12802	nCoV-2019_42_RIGHT	2	-
+MN908947.3	12710	12732	nCoV-2019_43_LEFT	1	+
+MN908947.3	13074	13096	nCoV-2019_43_RIGHT	1	-
+MN908947.3	13005	13027	nCoV-2019_44_LEFT	2	+
+MN908947.3	13007	13029	nCoV-2019_44_LEFT_alt3	2	+
+MN908947.3	13378	13400	nCoV-2019_44_RIGHT	2	-
+MN908947.3	13363	13385	nCoV-2019_44_RIGHT_alt0	2	-
+MN908947.3	13319	13344	nCoV-2019_45_LEFT	1	+
+MN908947.3	13307	13336	nCoV-2019_45_LEFT_alt2	1	+
+MN908947.3	13669	13699	nCoV-2019_45_RIGHT	1	-
+MN908947.3	13660	13689	nCoV-2019_45_RIGHT_alt7	1	-
+MN908947.3	13599	13621	nCoV-2019_46_LEFT	2	+
+MN908947.3	13602	13625	nCoV-2019_46_LEFT_alt1	2	+
+MN908947.3	13962	13984	nCoV-2019_46_RIGHT	2	-
+MN908947.3	13961	13984	nCoV-2019_46_RIGHT_alt2	2	-
+MN908947.3	13918	13946	nCoV-2019_47_LEFT	1	+
+MN908947.3	14271	14299	nCoV-2019_47_RIGHT	1	-
+MN908947.3	14207	14232	nCoV-2019_48_LEFT	2	+
+MN908947.3	14579	14601	nCoV-2019_48_RIGHT	2	-
+MN908947.3	14545	14570	nCoV-2019_49_LEFT	1	+
+MN908947.3	14898	14926	nCoV-2019_49_RIGHT	1	-
+MN908947.3	14865	14895	nCoV-2019_50_LEFT	2	+
+MN908947.3	15224	15246	nCoV-2019_50_RIGHT	2	-
+MN908947.3	15171	15193	nCoV-2019_51_LEFT	1	+
+MN908947.3	15538	15560	nCoV-2019_51_RIGHT	1	-
+MN908947.3	15481	15503	nCoV-2019_52_LEFT	2	+
+MN908947.3	15861	15886	nCoV-2019_52_RIGHT	2	-
+MN908947.3	15827	15851	nCoV-2019_53_LEFT	1	+
+MN908947.3	16186	16209	nCoV-2019_53_RIGHT	1	-
+MN908947.3	16118	16144	nCoV-2019_54_LEFT	2	+
+MN908947.3	16485	16510	nCoV-2019_54_RIGHT	2	-
+MN908947.3	16416	16444	nCoV-2019_55_LEFT	1	+
+MN908947.3	16804	16833	nCoV-2019_55_RIGHT	1	-
+MN908947.3	16748	16770	nCoV-2019_56_LEFT	2	+
+MN908947.3	17130	17152	nCoV-2019_56_RIGHT	2	-
+MN908947.3	17065	17087	nCoV-2019_57_LEFT	1	+
+MN908947.3	17430	17452	nCoV-2019_57_RIGHT	1	-
+MN908947.3	17381	17406	nCoV-2019_58_LEFT	2	+
+MN908947.3	17738	17761	nCoV-2019_58_RIGHT	2	-
+MN908947.3	17674	17697	nCoV-2019_59_LEFT	1	+
+MN908947.3	18036	18062	nCoV-2019_59_RIGHT	1	-
+MN908947.3	17966	17993	nCoV-2019_60_LEFT	2	+
+MN908947.3	18324	18348	nCoV-2019_60_RIGHT	2	-
+MN908947.3	18253	18275	nCoV-2019_61_LEFT	1	+
+MN908947.3	18650	18672	nCoV-2019_61_RIGHT	1	-
+MN908947.3	18596	18618	nCoV-2019_62_LEFT	2	+
+MN908947.3	18957	18979	nCoV-2019_62_RIGHT	2	-
+MN908947.3	18896	18918	nCoV-2019_63_LEFT	1	+
+MN908947.3	19275	19297	nCoV-2019_63_RIGHT	1	-
+MN908947.3	19204	19232	nCoV-2019_64_LEFT	2	+
+MN908947.3	19591	19616	nCoV-2019_64_RIGHT	2	-
+MN908947.3	19548	19570	nCoV-2019_65_LEFT	1	+
+MN908947.3	19911	19939	nCoV-2019_65_RIGHT	1	-
+MN908947.3	19844	19866	nCoV-2019_66_LEFT	2	+
+MN908947.3	20231	20255	nCoV-2019_66_RIGHT	2	-
+MN908947.3	20172	20200	nCoV-2019_67_LEFT	1	+
+MN908947.3	20542	20572	nCoV-2019_67_RIGHT	1	-
+MN908947.3	20472	20496	nCoV-2019_68_LEFT	2	+
+MN908947.3	20867	20890	nCoV-2019_68_RIGHT	2	-
+MN908947.3	20786	20813	nCoV-2019_69_LEFT	1	+
+MN908947.3	21146	21169	nCoV-2019_69_RIGHT	1	-
+MN908947.3	21075	21104	nCoV-2019_70_LEFT	2	+
+MN908947.3	21427	21455	nCoV-2019_70_RIGHT	2	-
+MN908947.3	21357	21386	nCoV-2019_71_LEFT	1	+
+MN908947.3	21716	21743	nCoV-2019_71_RIGHT	1	-
+MN908947.3	21658	21682	nCoV-2019_72_LEFT	2	+
+MN908947.3	22013	22038	nCoV-2019_72_RIGHT	2	-
+MN908947.3	21961	21990	nCoV-2019_73_LEFT	1	+
+MN908947.3	22324	22346	nCoV-2019_73_RIGHT	1	-
+MN908947.3	22262	22290	nCoV-2019_74_LEFT	2	+
+MN908947.3	22626	22650	nCoV-2019_74_RIGHT	2	-
+MN908947.3	22516	22542	nCoV-2019_75_LEFT	1	+
+MN908947.3	22877	22903	nCoV-2019_75_RIGHT	1	-
+MN908947.3	22797	22819	nCoV-2019_76_LEFT	2	+
+MN908947.3	22798	22821	nCoV-2019_76_LEFT_alt3	2	+
+MN908947.3	23192	23214	nCoV-2019_76_RIGHT	2	-
+MN908947.3	23189	23212	nCoV-2019_76_RIGHT_alt0	2	-
+MN908947.3	23122	23144	nCoV-2019_77_LEFT	1	+
+MN908947.3	23500	23522	nCoV-2019_77_RIGHT	1	-
+MN908947.3	23443	23466	nCoV-2019_78_LEFT	2	+
+MN908947.3	23822	23847	nCoV-2019_78_RIGHT	2	-
+MN908947.3	23789	23812	nCoV-2019_79_LEFT	1	+
+MN908947.3	24145	24169	nCoV-2019_79_RIGHT	1	-
+MN908947.3	24078	24100	nCoV-2019_80_LEFT	2	+
+MN908947.3	24443	24467	nCoV-2019_80_RIGHT	2	-
+MN908947.3	24391	24416	nCoV-2019_81_LEFT	1	+
+MN908947.3	24765	24789	nCoV-2019_81_RIGHT	1	-
+MN908947.3	24696	24721	nCoV-2019_82_LEFT	2	+
+MN908947.3	25052	25076	nCoV-2019_82_RIGHT	2	-
+MN908947.3	24978	25003	nCoV-2019_83_LEFT	1	+
+MN908947.3	25347	25369	nCoV-2019_83_RIGHT	1	-
+MN908947.3	25279	25301	nCoV-2019_84_LEFT	2	+
+MN908947.3	25646	25673	nCoV-2019_84_RIGHT	2	-
+MN908947.3	25601	25623	nCoV-2019_85_LEFT	1	+
+MN908947.3	25969	25994	nCoV-2019_85_RIGHT	1	-
+MN908947.3	25902	25924	nCoV-2019_86_LEFT	2	+
+MN908947.3	26290	26315	nCoV-2019_86_RIGHT	2	-
+MN908947.3	26197	26219	nCoV-2019_87_LEFT	1	+
+MN908947.3	26566	26590	nCoV-2019_87_RIGHT	1	-
+MN908947.3	26520	26542	nCoV-2019_88_LEFT	2	+
+MN908947.3	26890	26913	nCoV-2019_88_RIGHT	2	-
+MN908947.3	26835	26857	nCoV-2019_89_LEFT	1	+
+MN908947.3	26838	26860	nCoV-2019_89_LEFT_alt2	1	+
+MN908947.3	27202	27227	nCoV-2019_89_RIGHT	1	-
+MN908947.3	27190	27215	nCoV-2019_89_RIGHT_alt4	1	-
+MN908947.3	27141	27164	nCoV-2019_90_LEFT	2	+
+MN908947.3	27511	27533	nCoV-2019_90_RIGHT	2	-
+MN908947.3	27446	27471	nCoV-2019_91_LEFT	1	+
+MN908947.3	27825	27854	nCoV-2019_91_RIGHT	1	-
+MN908947.3	27784	27808	nCoV-2019_92_LEFT	2	+
+MN908947.3	28145	28172	nCoV-2019_92_RIGHT	2	-
+MN908947.3	28081	28104	nCoV-2019_93_LEFT	1	+
+MN908947.3	28442	28464	nCoV-2019_93_RIGHT	1	-
+MN908947.3	28394	28416	nCoV-2019_94_LEFT	2	+
+MN908947.3	28756	28779	nCoV-2019_94_RIGHT	2	-
+MN908947.3	28677	28699	nCoV-2019_95_LEFT	1	+
+MN908947.3	29041	29063	nCoV-2019_95_RIGHT	1	-
+MN908947.3	28985	29007	nCoV-2019_96_LEFT	2	+
+MN908947.3	29356	29378	nCoV-2019_96_RIGHT	2	-
+MN908947.3	29288	29316	nCoV-2019_97_LEFT	1	+
+MN908947.3	29665	29693	nCoV-2019_97_RIGHT	1	-
+MN908947.3	29486	29510	nCoV-2019_98_LEFT	2	+
+MN908947.3	29836	29866	nCoV-2019_98_RIGHT	2	-
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
index fcaeb24b..3edfbe99 100644
--- a/workflow/rules/common.smk
+++ b/workflow/rules/common.smk
@@ -355,9 +355,11 @@ def get_non_cov2_calls(from_caller="pangolin"):
     pattern = (
         "results/benchmarking/tables/strain-calls/non-cov2-{accession}.polished.strains.pangolin.csv"
         if from_caller == "pangolin"
-        else "results/benchmarking/tables/strain-calls/non-cov2-{accession}.strains.kallisto.tsv"
-        if from_caller == "kallisto"
-        else []
+        else (
+            "results/benchmarking/tables/strain-calls/non-cov2-{accession}.strains.kallisto.tsv"
+            if from_caller == "kallisto"
+            else []
+        )
     )
 
     if not pattern:
@@ -1113,18 +1115,22 @@ def get_fallbacks_for_report(fallback_type):
         if fallback_type == "pseudo":
             path = "results/{{date}}/contigs/pseudoassembled/{sample}.fasta"
             return [
-                path.format(sample=sample)
-                if has_pseudo_assembly(None, sample)
-                else "resources/genomes/main.fasta"
+                (
+                    path.format(sample=sample)
+                    if has_pseudo_assembly(None, sample)
+                    else "resources/genomes/main.fasta"
+                )
                 for sample in get_samples_for_date(wildcards.date)
             ]
 
         elif fallback_type == "consensus":
             path = "results/{{date}}/contigs/masked/consensus/{sample}.fasta"
             return [
-                path.format(sample=sample)
-                if has_consensus_assembly(None, sample)
-                else "resources/genomes/main.fasta"
+                (
+                    path.format(sample=sample)
+                    if has_consensus_assembly(None, sample)
+                    else "resources/genomes/main.fasta"
+                )
                 for sample in samples
             ]
 
@@ -1390,9 +1396,11 @@ def get_kallisto_quant_extra(wildcards, input):
         return get_if_testing("--single --fragment-length 250 --sd 47301")
 
     return (
-        f"--single --fragment-length {get_first_line(input.fragment_length)} --sd {get_first_line(input.standard_deviation)}"
-        if is_single_end(wildcards)
-        else "",
+        (
+            f"--single --fragment-length {get_first_line(input.fragment_length)} --sd {get_first_line(input.standard_deviation)}"
+            if is_single_end(wildcards)
+            else ""
+        ),
     )
 
 
diff --git a/workflow/rules/generate_output.smk b/workflow/rules/generate_output.smk
index 11899c10..e6286372 100644
--- a/workflow/rules/generate_output.smk
+++ b/workflow/rules/generate_output.smk
@@ -381,9 +381,11 @@ rule snakemake_reports_patient:
         "results/{date}/qc/laboratory/multiqc.html",
         "results/{date}/plots/coverage-reference-genome.png",
         "results/{date}/plots/coverage-assembled-genome.png",
-        lambda wildcards: "results/{date}/plots/primer-clipping-intervals.svg"
-        if any_sample_is_amplicon(wildcards)
-        else [],
+        lambda wildcards: (
+            "results/{date}/plots/primer-clipping-intervals.svg"
+            if any_sample_is_amplicon(wildcards)
+            else []
+        ),
         # 4. Assembly
         "results/{date}/filter-overview",
         "results/{date}/pangolin-call-overview",
diff --git a/workflow/rules/read_clipping.smk b/workflow/rules/read_clipping.smk
index 8d93acc7..bc41c220 100644
--- a/workflow/rules/read_clipping.smk
+++ b/workflow/rules/read_clipping.smk
@@ -22,7 +22,7 @@ rule samtools_sort:
 
 rule bed_to_bedpe:
     input:
-        check_bed_for_URL(config["preprocessing"]["amplicon-primers"]),
+        config["preprocessing"]["amplicon-primers"],
     output:
         "resources/primer.bedpe",
     log:
diff --git a/workflow/rules/ref.smk b/workflow/rules/ref.smk
index 31fa8502..1458b6ec 100644
--- a/workflow/rules/ref.smk
+++ b/workflow/rules/ref.smk
@@ -20,9 +20,11 @@ rule get_genome:
         "resources/genomes/{accession}.fasta",
     params:
         accession=(
-            lambda w: config["virus-reference-genome"]
-            if w.accession == "main"
-            else w.accession
+            lambda w: (
+                config["virus-reference-genome"]
+                if w.accession == "main"
+                else w.accession
+            )
         ),
     log:
         "logs/genomes/get-genome/{accession}.log",
diff --git a/workflow/rules/variant_calling.smk b/workflow/rules/variant_calling.smk
index 8682bc98..fdd358c1 100644
--- a/workflow/rules/variant_calling.smk
+++ b/workflow/rules/variant_calling.smk
@@ -75,9 +75,11 @@ rule longshot:
             "results/{date}/candidate-calls/ref~{reference}/{sample}.homopolymer-longshot.vcf"
         ),
     params:
-        reference_name=lambda w: config["virus-reference-genome"]
-        if w.reference == "main"
-        else f"{w.reference}.1",
+        reference_name=lambda w: (
+            config["virus-reference-genome"]
+            if w.reference == "main"
+            else f"{w.reference}.1"
+        ),
     log:
         "logs/{date}/longshot/ref~{reference}/{sample}.log",
     conda:
diff --git a/workflow/scripts/bed-to-bedpe.py b/workflow/scripts/bed-to-bedpe.py
index 4a3b343d..2f5e707f 100644
--- a/workflow/scripts/bed-to-bedpe.py
+++ b/workflow/scripts/bed-to-bedpe.py
@@ -4,10 +4,26 @@
 # except according to those terms.
 
 import pandas as pd
+import urllib.request
+
+
+# Function to check bed for url
+def check_bed_for_URL(bed_file):
+    if "https" in bed_file:
+        filename = bed_file.split("/")[-1]
+        filepath = "resources/{}".format(filename)
+        urllib.request.urlretrieve(bed_file, filepath)
+        return filepath
+    else:
+        return bed_file
+
+
+# Check bed file for URL
+bed_file = check_bed_for_URL(snakemake.input[0])
 
 # Function to create a bedpe file from a bed file
 bed_list = []
-with open(snakemake.input[0]) as f:
+with open(bed_file) as f:
     line = f.readlines()
     for name in line:
         bed_list.append(name.split())

From 3b81486692d71c19a287961b59b10419995e05e7 Mon Sep 17 00:00:00 2001
From: Hamdiye Uzuner <hamdiyeuzuner@gmail.com>
Date: Wed, 30 Oct 2024 08:59:32 +0100
Subject: [PATCH 7/7] fix log not being found by the system (#671)

---
 workflow/rules/read_clipping.smk | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/workflow/rules/read_clipping.smk b/workflow/rules/read_clipping.smk
index bc41c220..9c693e82 100644
--- a/workflow/rules/read_clipping.smk
+++ b/workflow/rules/read_clipping.smk
@@ -44,7 +44,6 @@ rule bamclipper:
         ),
     params:
         output_dir=get_output_dir,
-        cwd=lambda w: os.getcwd(),
         bed_path=lambda w, input: os.path.join(os.getcwd(), input.bedpe),
         bam=lambda w, input: os.path.basename(input.bam),
     log:
@@ -57,7 +56,7 @@ rule bamclipper:
         " cp {input.bai} {params.output_dir} &&"
         " cd {params.output_dir} &&"
         " bamclipper.sh -b {params.bam} -p {params.bed_path} -n {threads} -u 5 -d 5) "
-        " > {params.cwd}/{log} 2>&1"
+        " > {log} 2>&1"
 
 
 rule fgbio: