From 539c69f308940469061beba0e3f682ca93d684ed Mon Sep 17 00:00:00 2001
From: Daniel Lundin <matricaria.suaveolens@gmail.com>
Date: Mon, 28 Aug 2023 18:17:20 +0200
Subject: [PATCH] Updated tools to 2.9

---
 modules.json | 102 ++++++++++++++++++++++++++++++++++++++-------------
 1 file changed, 76 insertions(+), 26 deletions(-)

diff --git a/modules.json b/modules.json
index b557b53d..ea5f1e48 100644
--- a/modules.json
+++ b/modules.json
@@ -8,117 +8,163 @@
                     "bbmap/align": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bbmap/bbduk": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bbmap/bbnorm": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "bbmap/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cat/cat": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "cat/fastq": {
                         "branch": "master",
                         "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "fastqc": {
                         "branch": "master",
                         "git_sha": "bd8092b67b5103bdd52e300f75889442275c3117",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "hmmer/hmmsearch": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "multiqc": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "prodigal": {
                         "branch": "master",
                         "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "prokka": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "samtools/flagstat": {
                         "branch": "master",
                         "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
-                        "installed_by": ["bam_stats_samtools"]
+                        "installed_by": [
+                            "bam_stats_samtools"
+                        ]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
                         "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
-                        "installed_by": ["bam_stats_samtools"]
+                        "installed_by": [
+                            "bam_stats_samtools"
+                        ]
                     },
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["bam_sort_stats_samtools"]
+                        "installed_by": [
+                            "bam_sort_stats_samtools"
+                        ]
                     },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
-                        "installed_by": ["bam_sort_stats_samtools"]
+                        "installed_by": [
+                            "bam_sort_stats_samtools"
+                        ]
                     },
                     "samtools/stats": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": ["bam_stats_samtools"]
+                        "installed_by": [
+                            "bam_stats_samtools"
+                        ]
                     },
                     "seqtk/mergepe": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "spades": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "subread/featurecounts": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "transdecoder/longorf": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "transdecoder/predict": {
                         "branch": "master",
                         "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     },
                     "trimgalore": {
                         "branch": "master",
                         "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["modules"]
+                        "installed_by": [
+                            "modules"
+                        ]
                     }
                 }
             },
@@ -127,15 +173,19 @@
                     "bam_sort_stats_samtools": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": ["subworkflows"]
+                        "installed_by": [
+                            "subworkflows"
+                        ]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
                         "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
-                        "installed_by": ["bam_sort_stats_samtools"]
+                        "installed_by": [
+                            "bam_sort_stats_samtools"
+                        ]
                     }
                 }
             }
         }
     }
-}
+}
\ No newline at end of file