From 0270c0fbbbb09456d7823605e4285c4a2c5bbf40 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Tue, 10 Dec 2024 09:44:41 +0100
Subject: [PATCH 1/6] Add foldmason createdb (#7180)

* add first version module

* add test

* add tests

* add

* ass

* add

* up

* update containers

* update version

* update version easymsa

* Update modules/nf-core/foldmason/createdb/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/nf-core/foldmason/createdb/meta.yml

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/nf-core/foldmason/createdb/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/nf-core/foldmason/createdb/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

---------

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
---
 .../foldmason/createdb/environment.yml        |   5 +
 modules/nf-core/foldmason/createdb/main.nf    |  47 +++++++
 modules/nf-core/foldmason/createdb/meta.yml   |  48 +++++++
 .../foldmason/createdb/tests/main.nf.test     |  66 +++++++++
 .../createdb/tests/main.nf.test.snap          | 128 ++++++++++++++++++
 .../nf-core/foldmason/easymsa/environment.yml |   4 +-
 modules/nf-core/foldmason/easymsa/main.nf     |   5 +-
 .../foldmason/easymsa/tests/main.nf.test.snap |  32 ++---
 8 files changed, 315 insertions(+), 20 deletions(-)
 create mode 100644 modules/nf-core/foldmason/createdb/environment.yml
 create mode 100644 modules/nf-core/foldmason/createdb/main.nf
 create mode 100644 modules/nf-core/foldmason/createdb/meta.yml
 create mode 100644 modules/nf-core/foldmason/createdb/tests/main.nf.test
 create mode 100644 modules/nf-core/foldmason/createdb/tests/main.nf.test.snap

diff --git a/modules/nf-core/foldmason/createdb/environment.yml b/modules/nf-core/foldmason/createdb/environment.yml
new file mode 100644
index 00000000000..80d4dd371d9
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::foldmason=2.7bd21ed
diff --git a/modules/nf-core/foldmason/createdb/main.nf b/modules/nf-core/foldmason/createdb/main.nf
new file mode 100644
index 00000000000..c54b45f3f06
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/main.nf
@@ -0,0 +1,47 @@
+process FOLDMASON_CREATEDB {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a88d162c3f39a1518d48c3faec235e6fcde750586da868b62fc5f0a08a89aa9d/data' :
+            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
+
+    input:
+    tuple val(meta) , path(structures)
+
+    output:
+    tuple val(meta), path("${prefix}*"), emit: db
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    foldmason createdb \\
+        ${structures} \\
+        ${prefix} \\
+        $args \\
+        --threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/foldmason/createdb/meta.yml b/modules/nf-core/foldmason/createdb/meta.yml
new file mode 100644
index 00000000000..fd47efe2f90
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/meta.yml
@@ -0,0 +1,48 @@
+name: "foldmason_createdb"
+description: Creates a database for Foldmason.
+keywords:
+  - alignment
+  - MSA
+  - genomics
+  - structure
+tools:
+  - "foldmason":
+      description: "Multiple Protein Structure Alignment at Scale with FoldMason"
+      homepage: "https://github.com/steineggerlab/foldmason"
+      documentation: "https://github.com/steineggerlab/foldmason"
+      tool_dev_url: "https://github.com/steineggerlab/foldmason"
+      doi: "10.1101/2024.08.01.606130"
+      licence: ["GPL v3"]
+      identifier: biotools:foldmason
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - structures:
+        type: file
+        description: Input protein structures in `PDB` or `mmCIF` format.
+        pattern: "*.{pdb,mmcif}"
+
+output:
+  - db:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "${prefix}*":
+          type: file
+          description: All database files created by Foldmason
+          pattern: "*"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@luisas"
+maintainers:
+  - "@luisas"
diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test b/modules/nf-core/foldmason/createdb/tests/main.nf.test
new file mode 100644
index 00000000000..9ac567a7504
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test
@@ -0,0 +1,66 @@
+nextflow_process {
+
+    name "Test Process FOLDMASON_CREATEDB"
+    script "../main.nf"
+    process "FOLDMASON_CREATEDB"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "foldmason"
+    tag "foldmason/createdb"
+    tag  "untar"
+
+    setup {
+
+        run("UNTAR") {
+            script "../../../../../modules/nf-core/untar/main.nf"
+                process {
+                    """
+                        archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/af2_structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                        input[0] = Channel.of(tuple([id:'test'], archive))
+                    """
+                }
+        }
+    }
+
+    test("seatoxin") {
+
+        when {
+
+            process {
+                """
+                    input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success  },
+                { assert snapshot(process.out).match() }
+                )
+        }
+
+    }
+
+    test("seatoxin - stub ") {
+
+        when {
+
+            process {
+                """
+                    input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success  },
+                { assert snapshot(process.out).match() }
+                )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap
new file mode 100644
index 00000000000..dce5175dc90
--- /dev/null
+++ b/modules/nf-core/foldmason/createdb/tests/main.nf.test.snap
@@ -0,0 +1,128 @@
+{
+    "seatoxin - stub ": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test:md5,941321067eae439b4a8ccf6425d84751",
+                            "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015",
+                            "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274",
+                            "test.source:md5,7968a6cb6577ead230c31910380af948",
+                            "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9",
+                            "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
+                            "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba",
+                            "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16",
+                            "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4",
+                            "test_ss:md5,75d329b63c0383c3e43090ba89238e14",
+                            "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test:md5,941321067eae439b4a8ccf6425d84751",
+                            "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015",
+                            "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274",
+                            "test.source:md5,7968a6cb6577ead230c31910380af948",
+                            "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9",
+                            "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
+                            "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba",
+                            "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16",
+                            "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4",
+                            "test_ss:md5,75d329b63c0383c3e43090ba89238e14",
+                            "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-09T15:11:27.426024133"
+    },
+    "seatoxin": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test:md5,941321067eae439b4a8ccf6425d84751",
+                            "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015",
+                            "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274",
+                            "test.source:md5,7968a6cb6577ead230c31910380af948",
+                            "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9",
+                            "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
+                            "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba",
+                            "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16",
+                            "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4",
+                            "test_ss:md5,75d329b63c0383c3e43090ba89238e14",
+                            "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                ],
+                "db": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test:md5,941321067eae439b4a8ccf6425d84751",
+                            "test.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015",
+                            "test.lookup:md5,83047fddf9b6fbaa99f00cdf5a7dd274",
+                            "test.source:md5,7968a6cb6577ead230c31910380af948",
+                            "test_ca:md5,2738c516c1a15238a5c62c4ba6dee0b9",
+                            "test_ca.dbtype:md5,3fd85f9ee7ca8882c8caa747d0eef0b3",
+                            "test_ca.index:md5,cfdf544c3aa6d7e2034e4a01dac1d0ba",
+                            "test_h:md5,ab9ce99a99fc6ba6a98c4460410b6a16",
+                            "test_h.dbtype:md5,740bab4f9ec8808aedb68d6b1281aeb2",
+                            "test_h.index:md5,dc7c33ddb6a3dc54ad033120ef4c9af4",
+                            "test_ss:md5,75d329b63c0383c3e43090ba89238e14",
+                            "test_ss.dbtype:md5,f1d3ff8443297732862df21dc4e57262",
+                            "test_ss.index:md5,8d3c65fcda8b216fff2f1eb2c4dcc015"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6ebe56979a45b356d374cfc65c8a2b45"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-09T15:11:15.375341633"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/foldmason/easymsa/environment.yml b/modules/nf-core/foldmason/easymsa/environment.yml
index 64a5b3671d4..fa2909a9491 100644
--- a/modules/nf-core/foldmason/easymsa/environment.yml
+++ b/modules/nf-core/foldmason/easymsa/environment.yml
@@ -1,8 +1,6 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::foldmason=1.763a428
+  - bioconda::foldmason=2.7bd21ed
   - conda-forge::pigz=2.8
diff --git a/modules/nf-core/foldmason/easymsa/main.nf b/modules/nf-core/foldmason/easymsa/main.nf
index bb1737f05ef..b4870da0d10 100644
--- a/modules/nf-core/foldmason/easymsa/main.nf
+++ b/modules/nf-core/foldmason/easymsa/main.nf
@@ -3,7 +3,10 @@ process FOLDMASON_EASYMSA {
     label 'process_medium'
 
     conda "${moduleDir}/environment.yml"
-    container "community.wave.seqera.io/library/foldmason_pigz:54849036d93c89ed"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'oras://community.wave.seqera.io/library/foldmason_pigz:d8dfffbc768abe03':
+            'community.wave.seqera.io/library/foldmason_pigz:88809eb5649534b0' }"
+
 
     input:
     tuple val(meta) , path(pdbs)
diff --git a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap
index 384d2021284..4951f29bff3 100644
--- a/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap
+++ b/modules/nf-core/foldmason/easymsa/tests/main.nf.test.snap
@@ -19,7 +19,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ],
                 "msa_3di": [
                     [
@@ -38,7 +38,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ]
             }
         ],
@@ -46,7 +46,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T10:56:12.836231763"
+        "timestamp": "2024-12-09T15:22:29.135105042"
     },
     "Test on seatoxin dataset - uncompressed": {
         "content": [
@@ -68,7 +68,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ],
                 "msa_3di": [
                     [
@@ -87,7 +87,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ]
             }
         ],
@@ -95,7 +95,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T10:55:41.89060384"
+        "timestamp": "2024-12-09T15:21:46.797852094"
     },
     "Test on seatoxin dataset - compressed": {
         "content": [
@@ -117,7 +117,7 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ],
                 "msa_3di": [
                     [
@@ -136,7 +136,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ]
             }
         ],
@@ -144,7 +144,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T10:55:52.135344443"
+        "timestamp": "2024-12-09T15:21:58.958099076"
     },
     "Test on seatoxin dataset - guide_tree": {
         "content": [
@@ -154,7 +154,7 @@
                         {
                             "id": "test"
                         },
-                        "test_3di.fa:md5,46fa911158bb736c054dfad0378832b4"
+                        "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08"
                     ]
                 ],
                 "1": [
@@ -162,18 +162,18 @@
                         {
                             "id": "test"
                         },
-                        "test_aa.fa:md5,7ada48f0152342787a46505b9e8a2fae"
+                        "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ],
                 "msa_3di": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_3di.fa:md5,46fa911158bb736c054dfad0378832b4"
+                        "test_3di.fa:md5,7c591bb57218fc00fdcb0b48306afc08"
                     ]
                 ],
                 "msa_aa": [
@@ -181,11 +181,11 @@
                         {
                             "id": "test"
                         },
-                        "test_aa.fa:md5,7ada48f0152342787a46505b9e8a2fae"
+                        "test_aa.fa:md5,e18523697101ff5d474ce4b6d0188731"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,da4694171d1b0bb9559f7049334126ed"
+                    "versions.yml:md5,a29f8390ef8ef7b90ad85d99589d97e6"
                 ]
             }
         ],
@@ -193,6 +193,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T10:56:02.473496089"
+        "timestamp": "2024-12-09T15:22:11.0778334"
     }
 }
\ No newline at end of file

From d752b3edfab155e353c93ed868a24db2fc047ab0 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 10 Dec 2024 09:45:56 +0100
Subject: [PATCH 2/6] Update: deseq2/differential for upcoming improved
 standardisation of template modules (#7178)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

* Rename deseq_de.R to deseq2_differential.R for standaisation

* Update main.nf

---------

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/deseq2/differential/main.nf                     | 2 +-
 .../templates/{deseq_de.R => deseq2_differential.R}             | 0
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename modules/nf-core/deseq2/differential/templates/{deseq_de.R => deseq2_differential.R} (100%)

diff --git a/modules/nf-core/deseq2/differential/main.nf b/modules/nf-core/deseq2/differential/main.nf
index 4d25602f7d6..c76187b50b5 100644
--- a/modules/nf-core/deseq2/differential/main.nf
+++ b/modules/nf-core/deseq2/differential/main.nf
@@ -29,7 +29,7 @@ process DESEQ2_DIFFERENTIAL {
     task.ext.when == null || task.ext.when
 
     script:
-    template 'deseq_de.R'
+    template 'deseq2_differential.R'
 
     stub:
     """
diff --git a/modules/nf-core/deseq2/differential/templates/deseq_de.R b/modules/nf-core/deseq2/differential/templates/deseq2_differential.R
similarity index 100%
rename from modules/nf-core/deseq2/differential/templates/deseq_de.R
rename to modules/nf-core/deseq2/differential/templates/deseq2_differential.R

From 13e7d1046922381df90cd8fe9bee8c3e57ae8457 Mon Sep 17 00:00:00 2001
From: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Date: Tue, 10 Dec 2024 11:18:18 +0100
Subject: [PATCH 3/6] add stub test for samtools/mpileup (#7192)

add stub test
---
 modules/nf-core/samtools/mpileup/main.nf | 21 ++++++++++++++++++---
 1 file changed, 18 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf
index 8a3ff75eb4a..925c8244e09 100644
--- a/modules/nf-core/samtools/mpileup/main.nf
+++ b/modules/nf-core/samtools/mpileup/main.nf
@@ -6,13 +6,14 @@ process SAMTOOLS_MPILEUP {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
         'biocontainers/samtools:1.21--h50ea8bc_0' }"
+
     input:
     tuple val(meta), path(input), path(intervals)
     path  fasta
 
     output:
     tuple val(meta), path("*.mpileup.gz"), emit: mpileup
-    path  "versions.yml"                           , emit: versions
+    path  "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,15 +21,29 @@ process SAMTOOLS_MPILEUP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    intervals = intervals ? "-l ${intervals}" : ""
+    def intervals_arg = intervals ? "-l ${intervals}" : ""
     """
     samtools mpileup \\
         --fasta-ref $fasta \\
         --output ${prefix}.mpileup \\
         $args \\
-        $intervals \\
+        $intervals_arg \\
         $input
     bgzip ${prefix}.mpileup
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def intervals_arg = intervals ? "-l ${intervals}" : ""
+    """
+    touch ${prefix}.mpileup.gz
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')

From d3555a4a33ae94269b65f79f7066ac2fcb836005 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Tue, 10 Dec 2024 12:09:54 +0100
Subject: [PATCH 4/6] Add foldmason msa2lddtreport (#7191)

* add module

* add test

* update test

* up

* add

* update

* fix test

* Update modules/nf-core/foldmason/msa2lddtreport/main.nf

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

* Update modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>

---------

Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
---
 .../foldmason/msa2lddtreport/environment.yml  |   5 +
 .../nf-core/foldmason/msa2lddtreport/main.nf  |  52 +++++++++
 .../nf-core/foldmason/msa2lddtreport/meta.yml |  74 +++++++++++++
 .../msa2lddtreport/tests/main.nf.test         | 101 ++++++++++++++++++
 .../msa2lddtreport/tests/main.nf.test.snap    |  68 ++++++++++++
 5 files changed, 300 insertions(+)
 create mode 100644 modules/nf-core/foldmason/msa2lddtreport/environment.yml
 create mode 100644 modules/nf-core/foldmason/msa2lddtreport/main.nf
 create mode 100644 modules/nf-core/foldmason/msa2lddtreport/meta.yml
 create mode 100644 modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test
 create mode 100644 modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap

diff --git a/modules/nf-core/foldmason/msa2lddtreport/environment.yml b/modules/nf-core/foldmason/msa2lddtreport/environment.yml
new file mode 100644
index 00000000000..80d4dd371d9
--- /dev/null
+++ b/modules/nf-core/foldmason/msa2lddtreport/environment.yml
@@ -0,0 +1,5 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::foldmason=2.7bd21ed
diff --git a/modules/nf-core/foldmason/msa2lddtreport/main.nf b/modules/nf-core/foldmason/msa2lddtreport/main.nf
new file mode 100644
index 00000000000..e07a7552b73
--- /dev/null
+++ b/modules/nf-core/foldmason/msa2lddtreport/main.nf
@@ -0,0 +1,52 @@
+process FOLDMASON_MSA2LDDTREPORT {
+    tag "$meta.id"
+    label 'process_medium'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+            'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a8/a88d162c3f39a1518d48c3faec235e6fcde750586da868b62fc5f0a08a89aa9d/data' :
+            'community.wave.seqera.io/library/foldmason:2.7bd21ed--e7f739473ad6578d' }"
+    input:
+    tuple val(meta) , path(msa)
+    tuple val(meta2), path(db)
+    tuple val(meta3), path(pdbs)
+    tuple val(meta4), path(tree)
+
+    output:
+    tuple val(meta), path("${prefix}.html"), emit: html
+    path "versions.yml"                    , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def options_tree = tree ? "--guide-tree $tree" : ""
+    """
+    foldmason msa2lddtreport \\
+        ${meta.id} \\
+        ${msa} \\
+        ${prefix}.html \\
+        $args \\
+        ${options_tree} \\
+        --threads $task.cpus
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        foldmason: \$(foldmason | grep "foldmason Version:" | cut -d":" -f 2 | awk '{\$1=\$1;print}')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/foldmason/msa2lddtreport/meta.yml b/modules/nf-core/foldmason/msa2lddtreport/meta.yml
new file mode 100644
index 00000000000..cf9749acb07
--- /dev/null
+++ b/modules/nf-core/foldmason/msa2lddtreport/meta.yml
@@ -0,0 +1,74 @@
+name: "foldmason_msa2lddtreport"
+description: Renders a visualization report using foldmason
+keywords:
+  - alignment
+  - MSA
+  - genomics
+  - structure
+tools:
+  - "foldmason":
+      description: "Multiple Protein Structure Alignment at Scale with FoldMason"
+      homepage: "https://github.com/steineggerlab/foldmason"
+      documentation: "https://github.com/steineggerlab/foldmason"
+      tool_dev_url: "https://github.com/steineggerlab/foldmason"
+      doi: "10.1101/2024.08.01.606130"
+      licence: ["GPL v3"]
+      identifier: biotools:foldmason
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - msa:
+        type: file
+        description: Input alignment file.
+        pattern: "*.{fa,fasta,aln}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - db:
+        type: file
+        description: Input foldmason database.
+        pattern: "*"
+  - - meta3:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - pdbs:
+        type: file
+        description: Protein structures used for the visualization.
+        pattern: "*.{pdb}"
+  - - meta4:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - tree:
+        type: file
+        description: Guide tree used for the visualization .
+        pattern: "*.{nwk,dnd}"
+output:
+  - html:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "${prefix}.html":
+          type: file
+          description: HTML file with the foldmason visualization
+          pattern: "*.{html}"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@luisas"
+maintainers:
+  - "@luisas"
diff --git a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test
new file mode 100644
index 00000000000..b92c05d0704
--- /dev/null
+++ b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test
@@ -0,0 +1,101 @@
+nextflow_process {
+
+    name "Test Process FOLDMASON_MSA2LDDTREPORT"
+    script "../main.nf"
+    process "FOLDMASON_MSA2LDDTREPORT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "foldmason"
+    tag "foldmason/msa2lddtreport"
+    tag "foldmason/createdb"
+    tag "untar"
+    tag "famsa/guidetree"
+
+
+    setup{
+        run("UNTAR") {
+            script "../../../../../modules/nf-core/untar/main.nf"
+                process {
+                    """
+                    archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/af2_structures/seatoxin-ref.tar.gz", checkIfExists: true)
+                    input[0] = Channel.of(tuple([id:'test'], archive))
+                    """
+                }
+        }
+
+        run("FAMSA_GUIDETREE") {
+            script "../../../../../modules/nf-core/famsa/guidetree/main.nf"
+            process {
+                """
+                input[0] = [ [ id:'test_tree' ], // meta map
+                            file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        run("FOLDMASON_CREATEDB") {
+            script "../../../../../modules/nf-core/foldmason/createdb/main.nf"
+            process {
+                """
+                input[0] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                """
+            }
+        }
+
+
+    }
+
+    test("seatoxin") {
+
+
+        when {
+            process {
+                """
+                input[0] =[ [ id:'test' ], // meta map
+                            file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                            ]
+                input[1] = FOLDMASON_CREATEDB.out.db.collect{ meta, db -> db }.map{ db -> [[ id: 'test'], db]}
+                input[2] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                input[3] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_tree'], tree]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("seatixin - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] =[ [ id:'test_tree' ], // meta map
+                            file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true)
+                            ]
+                input[1] = FOLDMASON_CREATEDB.out.db.collect{ meta, db -> db }.map{ db -> [[ id: 'test'], db]}
+                input[2] = UNTAR.out.untar.map { meta,dir -> [meta, file(dir).listFiles().collect()]}
+                input[3] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_tree'], tree]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap
new file mode 100644
index 00000000000..da11cfad2df
--- /dev/null
+++ b/modules/nf-core/foldmason/msa2lddtreport/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "seatixin - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_tree"
+                        },
+                        "test_tree.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test_tree"
+                        },
+                        "test_tree.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T09:36:23.360594258"
+    },
+    "seatoxin": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.html:md5,7a90a8e674dc45ce4181498b8f53b519"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.html:md5,7a90a8e674dc45ce4181498b8f53b519"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,ed922d0faa7a3e3c8171a05296939468"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T09:54:03.711567262"
+    }
+}
\ No newline at end of file

From 9142b390538283705c084e4d612170972ff60326 Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Tue, 10 Dec 2024 12:30:25 +0100
Subject: [PATCH 5/6] MEGAHIT: fix single-end input (#7190)

* Fix space to command separated lst

* Put hte join the right place
---
 modules/nf-core/megahit/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf
index f6e50f94d43..db0612422bd 100644
--- a/modules/nf-core/megahit/main.nf
+++ b/modules/nf-core/megahit/main.nf
@@ -25,7 +25,7 @@ process MEGAHIT {
     def args = task.ext.args ?: ''
     def args2 = task.ext.args2 ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def reads_command = meta.single_end || !reads2 ? "-r ${reads1}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}"
+    def reads_command = meta.single_end || !reads2 ? "-r ${reads1.join(',')}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}"
     """
     megahit \\
         ${reads_command} \\

From 2edb63067971fb906749e96bf22b23a4ec892a62 Mon Sep 17 00:00:00 2001
From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com>
Date: Tue, 10 Dec 2024 17:33:26 +0530
Subject: [PATCH 6/6] Fix ci confirm pass (#7186)

* update confirm-pass jobs to correctly identify failed & cancelled

* touch gpu & cpu module to test

* bump NXF VER to 24.10.2
---
 .github/workflows/gpu-tests.yml               | 13 +++++---
 .github/workflows/nf-test.yml                 | 13 +++++---
 .../nf-core/bwameth/align/tests/main.nf.test  |  1 -
 modules/nf-core/parabricks/fq2bammeth/main.nf | 14 ++++----
 .../parabricks/fq2bammeth/tests/main.nf.test  |  9 +++---
 .../fq2bammeth/tests/main.nf.test.snap        | 32 +++++++++----------
 6 files changed, 46 insertions(+), 36 deletions(-)

diff --git a/.github/workflows/gpu-tests.yml b/.github/workflows/gpu-tests.yml
index 78667065a3b..2a341360f04 100644
--- a/.github/workflows/gpu-tests.yml
+++ b/.github/workflows/gpu-tests.yml
@@ -29,7 +29,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   nf-test-changes:
@@ -108,13 +108,18 @@ jobs:
     needs: [nf-test-gpu]
     if: always()
     steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
       - name: debug-print
         if: always()
         run: |
diff --git a/.github/workflows/nf-test.yml b/.github/workflows/nf-test.yml
index f8c71275bf9..036c40f0880 100644
--- a/.github/workflows/nf-test.yml
+++ b/.github/workflows/nf-test.yml
@@ -32,7 +32,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
-  NXF_VER: "24.10.1"
+  NXF_VER: "24.10.2"
 
 jobs:
   nf-test-changes:
@@ -110,13 +110,18 @@ jobs:
     needs: [nf-test]
     if: always()
     steps:
-      - name: All tests ok
-        if: ${{ success() || !contains(needs.*.result, 'failure') }}
-        run: exit 0
       - name: One or more tests failed
         if: ${{ contains(needs.*.result, 'failure') }}
         run: exit 1
 
+      - name: One or more tests cancelled
+        if: ${{ contains(needs.*.result, 'cancelled') }}
+        run: exit 1
+
+      - name: All tests ok
+        if: ${{ contains(needs.*.result, 'success') }}
+        run: exit 0
+
       - name: debug-print
         if: always()
         run: |
diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test
index 37dd4ad2b08..87195e0c31a 100644
--- a/modules/nf-core/bwameth/align/tests/main.nf.test
+++ b/modules/nf-core/bwameth/align/tests/main.nf.test
@@ -117,5 +117,4 @@ nextflow_process {
             )
         }
     }
-
 }
diff --git a/modules/nf-core/parabricks/fq2bammeth/main.nf b/modules/nf-core/parabricks/fq2bammeth/main.nf
index 44f266604bd..eb7ae685b71 100644
--- a/modules/nf-core/parabricks/fq2bammeth/main.nf
+++ b/modules/nf-core/parabricks/fq2bammeth/main.nf
@@ -27,14 +27,15 @@ process PARABRICKS_FQ2BAMMETH {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def in_fq_command = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads"
+    def args                = task.ext.args ?: ''
+    def prefix              = task.ext.prefix ?: "${meta.id}"
+    def in_fq_command       = meta.single_end ? "--in-se-fq $reads" : "--in-fq $reads"
     def known_sites_command = known_sites ? known_sites.collect{"--knownSites $it"}.join(' ') : ""
-    def known_sites_output = known_sites ? "--out-recal-file ${prefix}.table" : ""
-    def num_gpus = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
+    def known_sites_output  = known_sites ? "--out-recal-file ${prefix}.table" : ""
+    def num_gpus            = task.accelerator ? "--num-gpus $task.accelerator.request" : ''
     """
     ln -sf \$(readlink $fasta) $index/$fasta
+
     pbrun \\
         fq2bam_meth \\
         --ref $index/$fasta \\
@@ -44,6 +45,7 @@ process PARABRICKS_FQ2BAMMETH {
         $known_sites_output \\
         $num_gpus \\
         $args
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' )
@@ -55,11 +57,11 @@ process PARABRICKS_FQ2BAMMETH {
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "Parabricks module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.bam
     touch ${prefix}.bam.bai
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         pbrun: \$(echo \$(pbrun version 2>&1) | sed 's/^Please.* //' )
diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
index 459eb6317db..ce89e8cac9f 100644
--- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
+++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test
@@ -5,12 +5,12 @@ nextflow_process {
     process "PARABRICKS_FQ2BAMMETH"
     config "./nextflow.config"
 
+    tag "gpu"
     tag "bwameth/index"
     tag "modules"
     tag "parabricks"
     tag "parabricks/fq2bammeth"
     tag "modules_nfcore"
-    tag "gpu"
 
     setup {
         run("BWAMETH_INDEX") {
@@ -26,8 +26,7 @@ nextflow_process {
         }
     }
 
-
-    test("SRR389222 - fastq - se") {
+    test("SRR389222 single-end [fastq]") {
 
         when {
             process {
@@ -60,7 +59,7 @@ nextflow_process {
         }
     }
 
-    test("SRR389222 - fastq - se - stub") {
+    test("SRR389222 single-end [fastq] - stub") {
         options '-stub'
 
         when {
@@ -90,7 +89,7 @@ nextflow_process {
         }
     }
 
-    test("E. coli - fastq - pe - stub") {
+    test("E.coli paired-end [fastq] - stub") {
         options '-stub'
 
         when {
diff --git a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap
index cf06f28c7b3..21ae222c254 100644
--- a/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap
+++ b/modules/nf-core/parabricks/fq2bammeth/tests/main.nf.test.snap
@@ -1,5 +1,5 @@
 {
-    "SRR389222 - fastq - se - stub": {
+    "SRR389222 single-end [fastq] - stub": {
         "content": [
             {
                 "0": [
@@ -21,13 +21,13 @@
                     ]
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
-                    
+
                 ],
                 "4": [
-                    
+
                 ],
                 "5": [
                     "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
@@ -51,13 +51,13 @@
                     ]
                 ],
                 "bqsr_table": [
-                    
+
                 ],
                 "duplicate_metrics": [
-                    
+
                 ],
                 "qc_metrics": [
-                    
+
                 ],
                 "versions": [
                     "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
@@ -70,7 +70,7 @@
         },
         "timestamp": "2024-11-12T11:20:10.809580487"
     },
-    "E. coli - fastq - pe - stub": {
+    "E.coli paired-end [fastq] - stub": {
         "content": [
             {
                 "0": [
@@ -92,13 +92,13 @@
                     ]
                 ],
                 "2": [
-                    
+
                 ],
                 "3": [
-                    
+
                 ],
                 "4": [
-                    
+
                 ],
                 "5": [
                     "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
@@ -122,13 +122,13 @@
                     ]
                 ],
                 "bqsr_table": [
-                    
+
                 ],
                 "duplicate_metrics": [
-                    
+
                 ],
                 "qc_metrics": [
-                    
+
                 ],
                 "versions": [
                     "versions.yml:md5,882d996a64ad457fcaf85e3a75514baf"
@@ -141,7 +141,7 @@
         },
         "timestamp": "2024-11-12T11:20:18.927598721"
     },
-    "SRR389222 - fastq - se": {
+    "SRR389222 single-end [fastq]": {
         "content": [
             "a7f7ca7b5eb503ab58790d64a0273ed6",
             [
@@ -163,4 +163,4 @@
         },
         "timestamp": "2024-10-26T21:29:14.709022"
     }
-}
\ No newline at end of file
+}