Merge pull request #11 from muneebdev7/test

Major updates
muneebdev7 · Dec 31, 2024 · 2866562 · 2866562
2 parents 420dddd + fa79022
commit 2866562
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Showing 38 changed files with 894 additions and 855 deletions.
diff --git a/.gitignore b/.gitignore
@@ -7,3 +7,4 @@ testing/
 testing*
 *.pyc
 null/
+.vscode/
diff --git a/conf/modules.config b/conf/modules.config
@@ -31,7 +31,7 @@ process {
 
     withName: FASTP {
         ext.args   = [
-            "-q ${params.fastp_qualified_quality}",
+            "-q ${params.fastp_phred_quality}",
             "--cut_front",
             "--cut_tail",
             "--cut_mean_quality ${params.fastp_cut_mean_quality}",

diff --git a/modules.json b/modules.json
@@ -7,12 +7,12 @@
                 "nf-core": {
                     "bwa/index": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "2d20463181b1c38981a02e90d3084b5f9fa8d540",
                         "installed_by": ["modules"]
                     },
                     "fastp": {
@@ -22,12 +22,22 @@
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "08108058ea36a63f141c25c4e75f9f872a5b2296",
                         "installed_by": ["modules"]
                     },
                     "megahit": {
                         "branch": "master",
-                        "git_sha": "7755db15e36b30da564cd67fffdfe18a255092aa",
+                        "git_sha": "9142b390538283705c084e4d612170972ff60326",
+                        "installed_by": ["modules"]
+                    },
+                    "metabat2/jgisummarizebamcontigdepths": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
+                    "metabat2/metabat2": {
+                        "branch": "master",
+                        "git_sha": "cc217b9d56fe9d8aee2e152f6fc31ba8e5cba952",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
@@ -39,29 +49,24 @@
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
                         "installed_by": ["modules"]
-                    },
-                    "samtools/sort": {
-                        "branch": "master",
-                        "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
-                        "installed_by": ["modules"]
                     }
                 }
             },
             "subworkflows": {
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+                        "git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/nf-core/bwa/index/main.nf b/modules/nf-core/bwa/index/main.nf
diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml
diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf
diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf
diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml
diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml
diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf
diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml
diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf
diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml
diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test
-Original file line number
+Diff line change
@@ Expand Up / @@ -7,3 +7,4 @@ testing/ @@
     testing*
     *.pyc
     null/
+    .vscode/