From e2d4212ec42998445106d5ddfc7e41949b8fd4e4 Mon Sep 17 00:00:00 2001
From: Steven Stancic <srbija812@vet.k-state.edu>
Date: Fri, 28 Apr 2023 16:44:40 -0500
Subject: [PATCH 1/7] Ran module update and added org_path

---
 .nf-core.yml                                                    | 1 +
 modules/nf-core/{modules => }/blast/blastn/main.nf              | 0
 modules/nf-core/{modules => }/blast/blastn/meta.yml             | 0
 .../nf-core/{modules => }/custom/dumpsoftwareversions/main.nf   | 0
 .../nf-core/{modules => }/custom/dumpsoftwareversions/meta.yml  | 0
 .../dumpsoftwareversions/templates/dumpsoftwareversions.py      | 0
 modules/nf-core/{modules => }/fastqc/main.nf                    | 0
 modules/nf-core/{modules => }/fastqc/meta.yml                   | 0
 modules/nf-core/{modules => }/multiqc/main.nf                   | 0
 modules/nf-core/{modules => }/multiqc/meta.yml                  | 0
 modules/nf-core/{modules => }/seqkit/split2/main.nf             | 0
 modules/nf-core/{modules => }/seqkit/split2/meta.yml            | 0
 modules/nf-core/{modules => }/seqtk/mergepe/main.nf             | 0
 modules/nf-core/{modules => }/seqtk/mergepe/meta.yml            | 0
 modules/nf-core/{modules => }/seqtk/seq/main.nf                 | 0
 modules/nf-core/{modules => }/seqtk/seq/meta.yml                | 0
 nextflow_schema.json                                            | 2 +-
 17 files changed, 2 insertions(+), 1 deletion(-)
 rename modules/nf-core/{modules => }/blast/blastn/main.nf (100%)
 rename modules/nf-core/{modules => }/blast/blastn/meta.yml (100%)
 rename modules/nf-core/{modules => }/custom/dumpsoftwareversions/main.nf (100%)
 rename modules/nf-core/{modules => }/custom/dumpsoftwareversions/meta.yml (100%)
 rename modules/nf-core/{modules => }/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py (100%)
 rename modules/nf-core/{modules => }/fastqc/main.nf (100%)
 rename modules/nf-core/{modules => }/fastqc/meta.yml (100%)
 rename modules/nf-core/{modules => }/multiqc/main.nf (100%)
 rename modules/nf-core/{modules => }/multiqc/meta.yml (100%)
 rename modules/nf-core/{modules => }/seqkit/split2/main.nf (100%)
 rename modules/nf-core/{modules => }/seqkit/split2/meta.yml (100%)
 rename modules/nf-core/{modules => }/seqtk/mergepe/main.nf (100%)
 rename modules/nf-core/{modules => }/seqtk/mergepe/meta.yml (100%)
 rename modules/nf-core/{modules => }/seqtk/seq/main.nf (100%)
 rename modules/nf-core/{modules => }/seqtk/seq/meta.yml (100%)

diff --git a/.nf-core.yml b/.nf-core.yml
index fb7b8c6..7923114 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -55,3 +55,4 @@ lint:
     # Can't find minimum NF version and doesn't like the addition of 'dispatch'
     # to the events
   template_strings: false
+org_path: ksumngs
diff --git a/modules/nf-core/modules/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf
similarity index 100%
rename from modules/nf-core/modules/blast/blastn/main.nf
rename to modules/nf-core/blast/blastn/main.nf
diff --git a/modules/nf-core/modules/blast/blastn/meta.yml b/modules/nf-core/blast/blastn/meta.yml
similarity index 100%
rename from modules/nf-core/modules/blast/blastn/meta.yml
rename to modules/nf-core/blast/blastn/meta.yml
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
similarity index 100%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/main.nf
rename to modules/nf-core/custom/dumpsoftwareversions/main.nf
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
similarity index 100%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/meta.yml
rename to modules/nf-core/custom/dumpsoftwareversions/meta.yml
diff --git a/modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
similarity index 100%
rename from modules/nf-core/modules/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
rename to modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
diff --git a/modules/nf-core/modules/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
similarity index 100%
rename from modules/nf-core/modules/fastqc/main.nf
rename to modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/modules/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
similarity index 100%
rename from modules/nf-core/modules/fastqc/meta.yml
rename to modules/nf-core/fastqc/meta.yml
diff --git a/modules/nf-core/modules/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
similarity index 100%
rename from modules/nf-core/modules/multiqc/main.nf
rename to modules/nf-core/multiqc/main.nf
diff --git a/modules/nf-core/modules/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
similarity index 100%
rename from modules/nf-core/modules/multiqc/meta.yml
rename to modules/nf-core/multiqc/meta.yml
diff --git a/modules/nf-core/modules/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf
similarity index 100%
rename from modules/nf-core/modules/seqkit/split2/main.nf
rename to modules/nf-core/seqkit/split2/main.nf
diff --git a/modules/nf-core/modules/seqkit/split2/meta.yml b/modules/nf-core/seqkit/split2/meta.yml
similarity index 100%
rename from modules/nf-core/modules/seqkit/split2/meta.yml
rename to modules/nf-core/seqkit/split2/meta.yml
diff --git a/modules/nf-core/modules/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf
similarity index 100%
rename from modules/nf-core/modules/seqtk/mergepe/main.nf
rename to modules/nf-core/seqtk/mergepe/main.nf
diff --git a/modules/nf-core/modules/seqtk/mergepe/meta.yml b/modules/nf-core/seqtk/mergepe/meta.yml
similarity index 100%
rename from modules/nf-core/modules/seqtk/mergepe/meta.yml
rename to modules/nf-core/seqtk/mergepe/meta.yml
diff --git a/modules/nf-core/modules/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf
similarity index 100%
rename from modules/nf-core/modules/seqtk/seq/main.nf
rename to modules/nf-core/seqtk/seq/main.nf
diff --git a/modules/nf-core/modules/seqtk/seq/meta.yml b/modules/nf-core/seqtk/seq/meta.yml
similarity index 100%
rename from modules/nf-core/modules/seqtk/seq/meta.yml
rename to modules/nf-core/seqtk/seq/meta.yml
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 1e780d2..8950b97 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -109,7 +109,7 @@
             "properties": {
                 "blast_db": {
                     "type": "string",
-                    "default": null,
+                    "default": "None",
                     "fa_icon": "fas fa-database",
                     "description": "Path to a folder containing a BLAST nt database"
                 },

From 6460735486fd70e42fbf49e84a6137b66d2ed963 Mon Sep 17 00:00:00 2001
From: Steven Stancic <srbija812@vet.k-state.edu>
Date: Fri, 28 Apr 2023 16:45:34 -0500
Subject: [PATCH 2/7] Updated README.md to remove yasvap references

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index d0e68a8..8691c9a 100644
--- a/README.md
+++ b/README.md
@@ -51,7 +51,7 @@ nextflow run ksumngs/v-met               \
 ### Example: Illumina reads with a relatively complete Kraken2 database
 
 ```bash
-nextflow run ksumngs/yavsap          \
+nextflow run ksumngs/v-met          \
   -profile singularity               \
   --platform illumina                \
   --kraken2_db /databases/kraken2/nt \
@@ -61,7 +61,7 @@ nextflow run ksumngs/yavsap          \
 ### Example: Nanopore reads with a viral-only Kraken2 database
 
 ```bash
-nextflow run ksumngs/yavsap             \
+nextflow run ksumngs/v-met             \
   -profile podman                       \
   --platform nanopore                   \
   --kraken2_db /databases/kraken2/viral \

From 566cea107e048fb9543c82d488d9271bd8b135fa Mon Sep 17 00:00:00 2001
From: Steven Stancic <srbija812@vet.k-state.edu>
Date: Wed, 3 May 2023 13:04:54 -0500
Subject: [PATCH 3/7] Changed manifest to stop nf-core lint crash

---
 nextflow.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/nextflow.config b/nextflow.config
index 893961e..a0740d2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -8,7 +8,7 @@
 
 // Pipeline metadata
 manifest {
-    name              = 'v-met'
+    name              = 'ksumngs/v-met'
     author            = 'K-State Molecular NGS Lab'
     homePage          = 'https://ksumngs.github.io/v-met'
     description       = 'A bare-bones, ridiculously simple metagenomics pipeline for viruses'

From 235016835b04a04075ae2566111ebb26a2cc7fe3 Mon Sep 17 00:00:00 2001
From: Steven Stancic <srbija812@vet.k-state.edu>
Date: Wed, 3 May 2023 13:25:12 -0500
Subject: [PATCH 4/7] Updated python version in lint test

---
 .github/workflows/linting.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
index 271a51a..227eb4b 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/linting.yml
@@ -36,7 +36,7 @@ jobs:
 
       - uses: actions/setup-python@v1
         with:
-          python-version: "3.6"
+          python-version: "3.11.3"
           architecture: "x64"
 
       - name: Install dependencies

From 2d092615f9a2b546a4da141fd419f37e7fa4869d Mon Sep 17 00:00:00 2001
From: Steven Stancic <srbija812@vet.k-state.edu>
Date: Mon, 8 May 2023 13:15:24 -0500
Subject: [PATCH 5/7] Redid the folder structure

---
 modules.json                                  | 131 ++++++++++++------
 .../{nf-modules => }/cat/fastq/main.nf        |   2 +-
 .../{nf-modules => }/cat/fastq/meta.yml       |   0
 .../ksumngs/{nf-modules => }/kraken2/main.nf  |   0
 .../ksumngs/{nf-modules => }/kraken2/meta.yml |   0
 .../krakentools/extract/main.nf               |   0
 .../krakentools/extract/meta.yml              |   6 +-
 .../krakentools/kreport2krona/main.nf         |   0
 .../krakentools/kreport2krona/meta.yml        |  32 ++---
 .../{nf-modules => }/krona/importtext/main.nf |   0
 .../krona/importtext/meta.yml                 |   2 +-
 .../ksumngs/{nf-modules => }/nanofilt/main.nf |   0
 .../{nf-modules => }/nanofilt/meta.yml        |   3 +-
 .../ksumngs/{nf-modules => }/nanostat/main.nf |   0
 .../{nf-modules => }/nanostat/meta.yml        |   3 +-
 .../{nf-modules => }/trimmomatic/main.nf      |   0
 .../{nf-modules => }/trimmomatic/meta.yml     |   2 +-
 modules/nf-core/blast/blastn/main.nf          |   8 +-
 .../custom/dumpsoftwareversions/main.nf       |   8 +-
 .../custom/dumpsoftwareversions/meta.yml      |   2 +
 .../templates/dumpsoftwareversions.py         |  98 +++++++------
 modules/nf-core/fastqc/main.nf                |  54 ++++----
 modules/nf-core/multiqc/main.nf               |  34 ++++-
 modules/nf-core/multiqc/meta.yml              |  18 ++-
 modules/nf-core/seqkit/split2/main.nf         |   4 +-
 modules/nf-core/seqkit/split2/meta.yml        |  46 +++---
 modules/nf-core/seqtk/mergepe/main.nf         |   6 +-
 modules/nf-core/seqtk/seq/main.nf             |  10 +-
 modules/nf-core/seqtk/seq/meta.yml            |   2 +-
 nextflow.config                               |   2 +-
 nextflow_schema.json                          |   4 +-
 31 files changed, 283 insertions(+), 194 deletions(-)
 rename modules/ksumngs/{nf-modules => }/cat/fastq/main.nf (96%)
 rename modules/ksumngs/{nf-modules => }/cat/fastq/meta.yml (100%)
 rename modules/ksumngs/{nf-modules => }/kraken2/main.nf (100%)
 rename modules/ksumngs/{nf-modules => }/kraken2/meta.yml (100%)
 rename modules/ksumngs/{nf-modules => }/krakentools/extract/main.nf (100%)
 rename modules/ksumngs/{nf-modules => }/krakentools/extract/meta.yml (92%)
 rename modules/ksumngs/{nf-modules => }/krakentools/kreport2krona/main.nf (100%)
 rename modules/ksumngs/{nf-modules => }/krakentools/kreport2krona/meta.yml (50%)
 rename modules/ksumngs/{nf-modules => }/krona/importtext/main.nf (100%)
 rename modules/ksumngs/{nf-modules => }/krona/importtext/meta.yml (96%)
 rename modules/ksumngs/{nf-modules => }/nanofilt/main.nf (100%)
 rename modules/ksumngs/{nf-modules => }/nanofilt/meta.yml (98%)
 rename modules/ksumngs/{nf-modules => }/nanostat/main.nf (100%)
 rename modules/ksumngs/{nf-modules => }/nanostat/meta.yml (97%)
 rename modules/ksumngs/{nf-modules => }/trimmomatic/main.nf (100%)
 rename modules/ksumngs/{nf-modules => }/trimmomatic/meta.yml (97%)

diff --git a/modules.json b/modules.json
index 3e86b8e..f745cbd 100644
--- a/modules.json
+++ b/modules.json
@@ -1,54 +1,95 @@
 {
-    "name": "v-met",
+    "name": "ksumngs/v-met",
     "homePage": "https://ksumngs.github.io/v-met",
     "repos": {
-        "ksumngs/nf-modules": {
-            "cat/fastq": {
-                "git_sha": "da5728117c6caaee428ed8729e88b93abc60c5fc"
-            },
-            "kraken2": {
-                "git_sha": "e0b2138159eab5b54a4618f320895a308fcf53fa"
-            },
-            "krakentools/extract": {
-                "git_sha": "181a04778a81494dc71b1d68b514b43cfef1512c"
-            },
-            "krakentools/kreport2krona": {
-                "git_sha": "c6c9d4fad20eb77232756fc08403fbc4e9988ce2"
-            },
-            "krona/importtext": {
-                "git_sha": "f423673c57aba461cf16bd3bc628e36e33b20029"
-            },
-            "nanofilt": {
-                "git_sha": "8e2140d607a9bbbf82ddf1604609f22e7371f9fb"
-            },
-            "nanostat": {
-                "git_sha": "89fce539f438cc7109b85fb7a5b75d5091382d54"
-            },
-            "trimmomatic": {
-                "git_sha": "78eb5cef96c8bbe59838c03c281780da50cfdef2"
+        "https://github.com/ksumngs/nf-modules": {
+            "modules": {
+                "ksumngs": {
+                    "cat/fastq": {
+                        "branch": "update_nf",
+                        "git_sha": "f39d201931b5eecdc15d2605e3cad9751df462a9",
+                        "installed_by": ["modules"]
+                    },
+                    "kraken2": {
+                        "branch": "update_nf",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "krakentools/extract": {
+                        "branch": "update_nf",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "krakentools/kreport2krona": {
+                        "branch": "update_nf",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "krona/importtext": {
+                        "branch": "update_nf",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "nanofilt": {
+                        "branch": "update_nf",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "nanostat": {
+                        "branch": "update_nf",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    },
+                    "trimmomatic": {
+                        "branch": "update_nf",
+                        "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
+                        "installed_by": ["modules"]
+                    }
+                }
             }
         },
-        "nf-core/modules": {
-            "blast/blastn": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "custom/dumpsoftwareversions": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "fastqc": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "multiqc": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "seqkit/split2": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
-            },
-            "seqtk/mergepe": {
-                "git_sha": "e745e167c1020928ef20ea1397b6b4d230681b4d"
+        "https://github.com/nf-core/modules.git": {
+            "modules": {
+                "nf-core": {
+                    "blast/blastn": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "custom/dumpsoftwareversions": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "fastqc": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "multiqc": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "seqkit/split2": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "seqtk/mergepe": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    },
+                    "seqtk/seq": {
+                        "branch": "master",
+                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "installed_by": ["modules"]
+                    }
+                }
             },
-            "seqtk/seq": {
-                "git_sha": "1016c9bd1a7b23e31b8215b8c33095e733080735"
+            "subworkflows": {
+                "nf-core": {}
             }
         }
     }
diff --git a/modules/ksumngs/nf-modules/cat/fastq/main.nf b/modules/ksumngs/cat/fastq/main.nf
similarity index 96%
rename from modules/ksumngs/nf-modules/cat/fastq/main.nf
rename to modules/ksumngs/cat/fastq/main.nf
index e2d5020..d942d79 100644
--- a/modules/ksumngs/nf-modules/cat/fastq/main.nf
+++ b/modules/ksumngs/cat/fastq/main.nf
@@ -57,7 +57,7 @@ process CAT_FASTQ {
 
         cat <<-END_VERSIONS > versions.yml
         "${task.process}":
-            gzip: echo \$(gzip --version | head -n1 | sed 's/^gzip //')
+            gzip: \$(gzip --version | head -n1 | sed 's/^gzip //')
         END_VERSIONS
         """
     }
diff --git a/modules/ksumngs/nf-modules/cat/fastq/meta.yml b/modules/ksumngs/cat/fastq/meta.yml
similarity index 100%
rename from modules/ksumngs/nf-modules/cat/fastq/meta.yml
rename to modules/ksumngs/cat/fastq/meta.yml
diff --git a/modules/ksumngs/nf-modules/kraken2/main.nf b/modules/ksumngs/kraken2/main.nf
similarity index 100%
rename from modules/ksumngs/nf-modules/kraken2/main.nf
rename to modules/ksumngs/kraken2/main.nf
diff --git a/modules/ksumngs/nf-modules/kraken2/meta.yml b/modules/ksumngs/kraken2/meta.yml
similarity index 100%
rename from modules/ksumngs/nf-modules/kraken2/meta.yml
rename to modules/ksumngs/kraken2/meta.yml
diff --git a/modules/ksumngs/nf-modules/krakentools/extract/main.nf b/modules/ksumngs/krakentools/extract/main.nf
similarity index 100%
rename from modules/ksumngs/nf-modules/krakentools/extract/main.nf
rename to modules/ksumngs/krakentools/extract/main.nf
diff --git a/modules/ksumngs/nf-modules/krakentools/extract/meta.yml b/modules/ksumngs/krakentools/extract/meta.yml
similarity index 92%
rename from modules/ksumngs/nf-modules/krakentools/extract/meta.yml
rename to modules/ksumngs/krakentools/extract/meta.yml
index 859a1b6..fc6356b 100644
--- a/modules/ksumngs/nf-modules/krakentools/extract/meta.yml
+++ b/modules/ksumngs/krakentools/extract/meta.yml
@@ -9,7 +9,7 @@ tools:
       description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
       homepage: https://ccb.jhu.edu/software/krakentools/
       tool_dev_url: https://github.com/jenniferlu717/KrakenTools
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:
@@ -25,8 +25,8 @@ input:
       type: file
       description: Kraken output describing the classification of each reads
   - kreport:
-        type: file
-        description: Kraken report with aggregate classification stats
+      type: file
+      description: Kraken report with aggregate classification stats
   - taxids:
       type: string
       description: Space-separated list of taxonomic ids to extract
diff --git a/modules/ksumngs/nf-modules/krakentools/kreport2krona/main.nf b/modules/ksumngs/krakentools/kreport2krona/main.nf
similarity index 100%
rename from modules/ksumngs/nf-modules/krakentools/kreport2krona/main.nf
rename to modules/ksumngs/krakentools/kreport2krona/main.nf
diff --git a/modules/ksumngs/nf-modules/krakentools/kreport2krona/meta.yml b/modules/ksumngs/krakentools/kreport2krona/meta.yml
similarity index 50%
rename from modules/ksumngs/nf-modules/krakentools/kreport2krona/meta.yml
rename to modules/ksumngs/krakentools/kreport2krona/meta.yml
index 4342de8..aa4de6a 100644
--- a/modules/ksumngs/nf-modules/krakentools/kreport2krona/meta.yml
+++ b/modules/ksumngs/krakentools/kreport2krona/meta.yml
@@ -1,32 +1,27 @@
 name: krakentools_kreport2krona
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
+description: Takes a Kraken report file and prints out a krona-compatible TEXT file
 keywords:
-  - sort
+  - kraken
+  - krona
+  - metagenomics
+  - visualization
 tools:
   - krakentools:
-      ## TODO nf-core: Add a description and other details for the software below
       description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs.
-      homepage: None
-      documentation: None
-      tool_dev_url: None
-      doi: ""
-      licence: ['GPL v3']
+      homepage: https://github.com/jenniferlu717/KrakenTools
+      licence: ["GPL v3"]
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
+  - kreport:
       type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: Kraken report
+      pattern: "*.{txt,kreport}"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
   - meta:
       type: map
@@ -37,11 +32,10 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
-  - bam:
+  - krona:
       type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: Krona text file converted from Kraken report
+      pattern: "*.{krona}"
 
 authors:
   - "@MillironX"
diff --git a/modules/ksumngs/nf-modules/krona/importtext/main.nf b/modules/ksumngs/krona/importtext/main.nf
similarity index 100%
rename from modules/ksumngs/nf-modules/krona/importtext/main.nf
rename to modules/ksumngs/krona/importtext/main.nf
diff --git a/modules/ksumngs/nf-modules/krona/importtext/meta.yml b/modules/ksumngs/krona/importtext/meta.yml
similarity index 96%
rename from modules/ksumngs/nf-modules/krona/importtext/meta.yml
rename to modules/ksumngs/krona/importtext/meta.yml
index 9bf434b..12817e0 100644
--- a/modules/ksumngs/nf-modules/krona/importtext/meta.yml
+++ b/modules/ksumngs/krona/importtext/meta.yml
@@ -8,7 +8,7 @@ tools:
   - krona:
       description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files.
       homepage: https://github.com/marbl/Krona/wiki
-      licence: ['BSD']
+      licence: ["BSD"]
 
 input:
   - krona:
diff --git a/modules/ksumngs/nf-modules/nanofilt/main.nf b/modules/ksumngs/nanofilt/main.nf
similarity index 100%
rename from modules/ksumngs/nf-modules/nanofilt/main.nf
rename to modules/ksumngs/nanofilt/main.nf
diff --git a/modules/ksumngs/nf-modules/nanofilt/meta.yml b/modules/ksumngs/nanofilt/meta.yml
similarity index 98%
rename from modules/ksumngs/nf-modules/nanofilt/meta.yml
rename to modules/ksumngs/nanofilt/meta.yml
index da1c439..c5546c8 100644
--- a/modules/ksumngs/nf-modules/nanofilt/meta.yml
+++ b/modules/ksumngs/nanofilt/meta.yml
@@ -8,7 +8,7 @@ tools:
       homepage: https://gigabaseorgigabyte.wordpress.com/2017/06/05/trimming-and-filtering-oxford-nanopore-sequencing-reads/
       tool_dev_url: https://github.com/wdecoster/nanofilt
       doi: "10.1093/bioinformatics/bty149"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:
@@ -40,6 +40,5 @@ output:
       description: File with stats on filtered reads
       pattern: "*.{log}"
 
-
 authors:
   - "@MillironX"
diff --git a/modules/ksumngs/nf-modules/nanostat/main.nf b/modules/ksumngs/nanostat/main.nf
similarity index 100%
rename from modules/ksumngs/nf-modules/nanostat/main.nf
rename to modules/ksumngs/nanostat/main.nf
diff --git a/modules/ksumngs/nf-modules/nanostat/meta.yml b/modules/ksumngs/nanostat/meta.yml
similarity index 97%
rename from modules/ksumngs/nf-modules/nanostat/meta.yml
rename to modules/ksumngs/nanostat/meta.yml
index 2f5718e..a447b71 100644
--- a/modules/ksumngs/nf-modules/nanostat/meta.yml
+++ b/modules/ksumngs/nanostat/meta.yml
@@ -8,7 +8,7 @@ tools:
       description: Calculate statistics for Oxford Nanopore sequencing data and alignments
       homepage: https://github.com/wdecoster/nanostat
       doi: "10.1093/bioinformatics/bty149"
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:
@@ -36,6 +36,5 @@ output:
       description: Read/alignment statistics report
       pattern: "*.{log}"
 
-
 authors:
   - "@MillironX"
diff --git a/modules/ksumngs/nf-modules/trimmomatic/main.nf b/modules/ksumngs/trimmomatic/main.nf
similarity index 100%
rename from modules/ksumngs/nf-modules/trimmomatic/main.nf
rename to modules/ksumngs/trimmomatic/main.nf
diff --git a/modules/ksumngs/nf-modules/trimmomatic/meta.yml b/modules/ksumngs/trimmomatic/meta.yml
similarity index 97%
rename from modules/ksumngs/nf-modules/trimmomatic/meta.yml
rename to modules/ksumngs/trimmomatic/meta.yml
index 5a1d49a..739eddc 100644
--- a/modules/ksumngs/nf-modules/trimmomatic/meta.yml
+++ b/modules/ksumngs/trimmomatic/meta.yml
@@ -8,7 +8,7 @@ tools:
       homepage: http://www.usadellab.org/cms/?page=trimmomatic
       tool_dev_url: https://github.com/usadellab/Trimmomatic
       doi: "10.1093/bioinformatics/btu170"
-      licence: ['GPL v3']
+      licence: ["GPL v3"]
 
 input:
   - meta:
diff --git a/modules/nf-core/blast/blastn/main.nf b/modules/nf-core/blast/blastn/main.nf
index b85f6c8..9a1f3a5 100644
--- a/modules/nf-core/blast/blastn/main.nf
+++ b/modules/nf-core/blast/blastn/main.nf
@@ -2,10 +2,10 @@ process BLAST_BLASTN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::blast=2.12.0' : null)
+    conda "bioconda::blast=2.13.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/blast:2.12.0--pl5262h3289130_0' :
-        'quay.io/biocontainers/blast:2.12.0--pl5262h3289130_0' }"
+        'https://depot.galaxyproject.org/singularity/blast:2.13.0--hf3cf87c_0' :
+        'biocontainers/blast:2.13.0--hf3cf87c_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -22,7 +22,7 @@ process BLAST_BLASTN {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    DB=`find -L ./ -name "*.ndb" | sed 's/.ndb//'`
+    DB=`find -L ./ -name "*.ndb" | sed 's/\\.ndb\$//'`
     blastn \\
         -num_threads $task.cpus \\
         -db \$DB \\
diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf
index 327d510..ebc8727 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/main.nf
+++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf
@@ -1,11 +1,11 @@
 process CUSTOM_DUMPSOFTWAREVERSIONS {
-    label 'process_low'
+    label 'process_single'
 
     // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container
-    conda (params.enable_conda ? "bioconda::multiqc=1.11" : null)
+    conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
     path versions
diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
index 60b546a..c32657d 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml
+++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml
@@ -1,7 +1,9 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: custom_dumpsoftwareversions
 description: Custom module used to dump software versions within the nf-core pipeline template
 keywords:
   - custom
+  - dump
   - version
 tools:
   - custom:
diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
index d139039..da03340 100644
--- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
+++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py
@@ -1,11 +1,16 @@
 #!/usr/bin/env python
 
+
+"""Provide functions to merge multiple versions.yml files."""
+
+
 import yaml
 import platform
 from textwrap import dedent
 
 
 def _make_versions_html(versions):
+    """Generate a tabular HTML output of all versions for MultiQC."""
     html = [
         dedent(
             """\\
@@ -44,46 +49,53 @@ def _make_versions_html(versions):
     return "\\n".join(html)
 
 
-versions_this_module = {}
-versions_this_module["${task.process}"] = {
-    "python": platform.python_version(),
-    "yaml": yaml.__version__,
-}
-
-with open("$versions") as f:
-    versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
-
-# aggregate versions by the module name (derived from fully-qualified process name)
-versions_by_module = {}
-for process, process_versions in versions_by_process.items():
-    module = process.split(":")[-1]
-    try:
-        assert versions_by_module[module] == process_versions, (
-            "We assume that software versions are the same between all modules. "
-            "If you see this error-message it means you discovered an edge-case "
-            "and should open an issue in nf-core/tools. "
-        )
-    except KeyError:
-        versions_by_module[module] = process_versions
-
-versions_by_module["Workflow"] = {
-    "Nextflow": "$workflow.nextflow.version",
-    "$workflow.manifest.name": "$workflow.manifest.version",
-}
-
-versions_mqc = {
-    "id": "software_versions",
-    "section_name": "${workflow.manifest.name} Software Versions",
-    "section_href": "https://github.com/${workflow.manifest.name}",
-    "plot_type": "html",
-    "description": "are collected at run time from the software output.",
-    "data": _make_versions_html(versions_by_module),
-}
-
-with open("software_versions.yml", "w") as f:
-    yaml.dump(versions_by_module, f, default_flow_style=False)
-with open("software_versions_mqc.yml", "w") as f:
-    yaml.dump(versions_mqc, f, default_flow_style=False)
-
-with open("versions.yml", "w") as f:
-    yaml.dump(versions_this_module, f, default_flow_style=False)
+def main():
+    """Load all version files and generate merged output."""
+    versions_this_module = {}
+    versions_this_module["${task.process}"] = {
+        "python": platform.python_version(),
+        "yaml": yaml.__version__,
+    }
+
+    with open("$versions") as f:
+        versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module
+
+    # aggregate versions by the module name (derived from fully-qualified process name)
+    versions_by_module = {}
+    for process, process_versions in versions_by_process.items():
+        module = process.split(":")[-1]
+        try:
+            if versions_by_module[module] != process_versions:
+                raise AssertionError(
+                    "We assume that software versions are the same between all modules. "
+                    "If you see this error-message it means you discovered an edge-case "
+                    "and should open an issue in nf-core/tools. "
+                )
+        except KeyError:
+            versions_by_module[module] = process_versions
+
+    versions_by_module["Workflow"] = {
+        "Nextflow": "$workflow.nextflow.version",
+        "$workflow.manifest.name": "$workflow.manifest.version",
+    }
+
+    versions_mqc = {
+        "id": "software_versions",
+        "section_name": "${workflow.manifest.name} Software Versions",
+        "section_href": "https://github.com/${workflow.manifest.name}",
+        "plot_type": "html",
+        "description": "are collected at run time from the software output.",
+        "data": _make_versions_html(versions_by_module),
+    }
+
+    with open("software_versions.yml", "w") as f:
+        yaml.dump(versions_by_module, f, default_flow_style=False)
+    with open("software_versions_mqc.yml", "w") as f:
+        yaml.dump(versions_mqc, f, default_flow_style=False)
+
+    with open("versions.yml", "w") as f:
+        yaml.dump(versions_this_module, f, default_flow_style=False)
+
+
+if __name__ == "__main__":
+    main()
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
index ed6b8c5..07d5e43 100644
--- a/modules/nf-core/fastqc/main.nf
+++ b/modules/nf-core/fastqc/main.nf
@@ -2,10 +2,10 @@ process FASTQC {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::fastqc=0.11.9" : null)
+    conda "bioconda::fastqc=0.11.9"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/fastqc:0.11.9--0' :
-        'quay.io/biocontainers/fastqc:0.11.9--0' }"
+        'biocontainers/fastqc:0.11.9--0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -20,28 +20,32 @@ process FASTQC {
 
     script:
     def args = task.ext.args ?: ''
-    // Add soft-links to original FastQs for consistent naming in pipeline
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if (meta.single_end) {
-        """
-        [ ! -f  ${prefix}.fastq.gz ] && ln -s $reads ${prefix}.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    } else {
-        """
-        [ ! -f  ${prefix}_1.fastq.gz ] && ln -s ${reads[0]} ${prefix}_1.fastq.gz
-        [ ! -f  ${prefix}_2.fastq.gz ] && ln -s ${reads[1]} ${prefix}_2.fastq.gz
-        fastqc $args --threads $task.cpus ${prefix}_1.fastq.gz ${prefix}_2.fastq.gz
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
-        END_VERSIONS
-        """
-    }
+    // Make list of old name and new name pairs to use for renaming in the bash while loop
+    def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] }
+    def rename_to = old_new_pairs*.join(' ').join(' ')
+    def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ')
+    """
+    printf "%s %s\\n" $rename_to | while read old_name new_name; do
+        [ -f "\${new_name}" ] || ln -s \$old_name \$new_name
+    done
+    fastqc $args --threads $task.cpus $renamed_files
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+    touch ${prefix}.zip
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqc: \$( fastqc --version | sed -e "s/FastQC v//g" )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
index 1264aac..1fc387b 100644
--- a/modules/nf-core/multiqc/main.nf
+++ b/modules/nf-core/multiqc/main.nf
@@ -1,13 +1,16 @@
 process MULTIQC {
-    label 'process_medium'
+    label 'process_single'
 
-    conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null)
+    conda "bioconda::multiqc=1.14"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' :
-        'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' :
+        'biocontainers/multiqc:1.14--pyhdfd78af_0' }"
 
     input:
-    path multiqc_files
+    path  multiqc_files, stageAs: "?/*"
+    path(multiqc_config)
+    path(extra_multiqc_config)
+    path(multiqc_logo)
 
     output:
     path "*multiqc_report.html", emit: report
@@ -20,8 +23,27 @@ process MULTIQC {
 
     script:
     def args = task.ext.args ?: ''
+    def config = multiqc_config ? "--config $multiqc_config" : ''
+    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
     """
-    multiqc -f $args .
+    multiqc \\
+        --force \\
+        $args \\
+        $config \\
+        $extra_config \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    touch multiqc_data
+    touch multiqc_plots
+    touch multiqc_report.html
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
index 6fa891e..f93b5ee 100644
--- a/modules/nf-core/multiqc/meta.yml
+++ b/modules/nf-core/multiqc/meta.yml
@@ -1,3 +1,4 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: MultiQC
 description: Aggregate results from bioinformatics analyses across many samples into a single report
 keywords:
@@ -12,18 +13,32 @@ tools:
       homepage: https://multiqc.info/
       documentation: https://multiqc.info/docs/
       licence: ["GPL-3.0-or-later"]
+
 input:
   - multiqc_files:
       type: file
       description: |
         List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - multiqc_config:
+      type: file
+      description: Optional config yml for MultiQC
+      pattern: "*.{yml,yaml}"
+  - extra_multiqc_config:
+      type: file
+      description: Second optional config yml for MultiQC. Will override common sections in multiqc_config.
+      pattern: "*.{yml,yaml}"
+  - multiqc_logo:
+      type: file
+      description: Optional logo file for MultiQC
+      pattern: "*.{png}"
+
 output:
   - report:
       type: file
       description: MultiQC report file
       pattern: "multiqc_report.html"
   - data:
-      type: dir
+      type: directory
       description: MultiQC data dir
       pattern: "multiqc_data"
   - plots:
@@ -38,3 +53,4 @@ authors:
   - "@abhi18av"
   - "@bunop"
   - "@drpatelh"
+  - "@jfy133"
diff --git a/modules/nf-core/seqkit/split2/main.nf b/modules/nf-core/seqkit/split2/main.nf
index ff91d86..0cd0926 100644
--- a/modules/nf-core/seqkit/split2/main.nf
+++ b/modules/nf-core/seqkit/split2/main.nf
@@ -2,10 +2,10 @@ process SEQKIT_SPLIT2 {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? 'bioconda::seqkit=2.1.0' : null)
+    conda "bioconda::seqkit=2.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/seqkit:2.1.0--h9ee0642_0' :
-        'quay.io/biocontainers/seqkit:2.1.0--h9ee0642_0' }"
+        'biocontainers/seqkit:2.1.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/seqkit/split2/meta.yml b/modules/nf-core/seqkit/split2/meta.yml
index 91c74b0..ac38606 100644
--- a/modules/nf-core/seqkit/split2/meta.yml
+++ b/modules/nf-core/seqkit/split2/meta.yml
@@ -5,35 +5,35 @@ keywords:
   - fastq
 tools:
   - seqkit:
-    description: |
-      Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
-    homepage: https://github.com/shenwei356/seqkit
-    documentation: https://bioinf.shenwei.me/seqkit/
-    doi: 10.1371/journal.pone.0163962
-    licence: ["MIT"]
+      description: |
+        Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
+      homepage: https://github.com/shenwei356/seqkit
+      documentation: https://bioinf.shenwei.me/seqkit/
+      doi: 10.1371/journal.pone.0163962
+      licence: ["MIT"]
 input:
   - meta:
-    type: map
-    description: |
-      Groovy Map containing sample information
-      e.g. [ id:'test', single_end:false ]
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - reads:
-    type: file
-    description: FastQ files
-    pattern: "*.{fq.gz/fastq.gz}"
+      type: file
+      description: FastQ files
+      pattern: "*.{fq.gz/fastq.gz}"
 output:
   - meta:
-    type: map
-    description: |
-      Groovy Map containing sample information
-      e.g. [ id:'test', single_end:false ]
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
   - reads:
-    type: file
-    description: Split fastq files
-    pattern: "*.{fq.gz/fastq.gz}"
+      type: file
+      description: Split fastq files
+      pattern: "*.{fq.gz/fastq.gz}"
   - versions:
-    type: file
-    description: File containing software versions
-    pattern: "versions.yml"
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
 authors:
   - "@FriederikeHanssen"
diff --git a/modules/nf-core/seqtk/mergepe/main.nf b/modules/nf-core/seqtk/mergepe/main.nf
index 519a4ab..6a4362e 100644
--- a/modules/nf-core/seqtk/mergepe/main.nf
+++ b/modules/nf-core/seqtk/mergepe/main.nf
@@ -1,11 +1,11 @@
 process SEQTK_MERGEPE {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
+    conda "bioconda::seqtk=1.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
-        'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
+        'biocontainers/seqtk:1.3--h5bf99c6_3' }"
 
     input:
     tuple val(meta), path(reads)
diff --git a/modules/nf-core/seqtk/seq/main.nf b/modules/nf-core/seqtk/seq/main.nf
index 1fb0300..c278592 100644
--- a/modules/nf-core/seqtk/seq/main.nf
+++ b/modules/nf-core/seqtk/seq/main.nf
@@ -1,11 +1,11 @@
 process SEQTK_SEQ {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
-    conda (params.enable_conda ? "bioconda::seqtk=1.3" : null)
+    conda "bioconda::seqtk=1.3"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' :
-        'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }"
+        'biocontainers/seqtk:1.3--h5bf99c6_3' }"
 
     input:
     tuple val(meta), path(fastx)
@@ -33,8 +33,8 @@ process SEQTK_SEQ {
         gzip -c > ${prefix}.seqtk-seq.${extension}.gz
 
     cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    "${task.process}":
+        seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/seqtk/seq/meta.yml b/modules/nf-core/seqtk/seq/meta.yml
index ac32162..3986257 100644
--- a/modules/nf-core/seqtk/seq/meta.yml
+++ b/modules/nf-core/seqtk/seq/meta.yml
@@ -8,7 +8,7 @@ tools:
       homepage: https://github.com/lh3/seqtk
       documentation: https://docs.csc.fi/apps/seqtk/
       tool_dev_url: https://github.com/lh3/seqtk
-      licence: ['MIT']
+      licence: ["MIT"]
 
 input:
   - meta:
diff --git a/nextflow.config b/nextflow.config
index a0740d2..c041670 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,7 +15,7 @@ manifest {
     mainScript        = 'main.nf'
     nextflowVersion   = '!>=21.10.6'
     version           = '1.0.1'
-    recurseSubmodules = true
+    //recurseSubmodules = true
 }
 
 // Capture exit codes from upstream processes when piping
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 8950b97..9fbe6b7 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -1,7 +1,7 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/v-met/master/nextflow_schema.json",
-    "title": "v-met pipeline parameters",
+    "$id": "https://raw.githubusercontent.com/ksumngs/v-met/master/nextflow_schema.json",
+    "title": "ksumngs/v-met pipeline parameters",
     "description": "A bare-bones, ridiculously simple metagenomics pipeline for viruses",
     "type": "object",
     "definitions": {

From f8d7e8a155cbfb953ef9575ddca2d33445d16cc6 Mon Sep 17 00:00:00 2001
From: Steven Stancic <srbija812@vet.k-state.edu>
Date: Mon, 8 May 2023 13:48:13 -0500
Subject: [PATCH 6/7] Allowed linting of manifest.name

---
 .nf-core.yml    | 4 ++--
 nextflow.config | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 7923114..6239e20 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -29,10 +29,10 @@ lint:
     # We don't use AWS
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
-  nextflow_config: false
+  nextflow_config:
   # Currently not supported, but hopefully soon!
   # See https://github.com/nf-core/tools/issues/1031
-  # - mainfest.name
+    - mainfest.name
   # - manifest.homePage
   files_unchanged:
     - .markdownlint.yml
diff --git a/nextflow.config b/nextflow.config
index c041670..a0740d2 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,7 +15,7 @@ manifest {
     mainScript        = 'main.nf'
     nextflowVersion   = '!>=21.10.6'
     version           = '1.0.1'
-    //recurseSubmodules = true
+    recurseSubmodules = true
 }
 
 // Capture exit codes from upstream processes when piping

From 5e51f2a0d77e0d9943492bdb02180f9e39459d31 Mon Sep 17 00:00:00 2001
From: Steven Stancic <srbija812@vet.k-state.edu>
Date: Mon, 8 May 2023 13:51:50 -0500
Subject: [PATCH 7/7] Updated modules.json to target master branch

---
 modules.json | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/modules.json b/modules.json
index f745cbd..69dda78 100644
--- a/modules.json
+++ b/modules.json
@@ -6,42 +6,42 @@
             "modules": {
                 "ksumngs": {
                     "cat/fastq": {
-                        "branch": "update_nf",
+                        "branch": "master",
                         "git_sha": "f39d201931b5eecdc15d2605e3cad9751df462a9",
                         "installed_by": ["modules"]
                     },
                     "kraken2": {
-                        "branch": "update_nf",
+                        "branch": "master",
                         "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
                         "installed_by": ["modules"]
                     },
                     "krakentools/extract": {
-                        "branch": "update_nf",
+                        "branch": "master",
                         "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
                         "installed_by": ["modules"]
                     },
                     "krakentools/kreport2krona": {
-                        "branch": "update_nf",
+                        "branch": "master",
                         "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
                         "installed_by": ["modules"]
                     },
                     "krona/importtext": {
-                        "branch": "update_nf",
+                        "branch": "master",
                         "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
                         "installed_by": ["modules"]
                     },
                     "nanofilt": {
-                        "branch": "update_nf",
+                        "branch": "master",
                         "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
                         "installed_by": ["modules"]
                     },
                     "nanostat": {
-                        "branch": "update_nf",
+                        "branch": "master",
                         "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
                         "installed_by": ["modules"]
                     },
                     "trimmomatic": {
-                        "branch": "update_nf",
+                        "branch": "master",
                         "git_sha": "8098c3fd301bcc759156e5fd2c84c5b19c2ca9d2",
                         "installed_by": ["modules"]
                     }