fix(qc): add procps-ng to QC containers and fix contributors manifest

CI on PR nf-core#205 surfaced two lint failures and container failures:

- nf-core lint: the three Altos contributor entries in the manifest had a
  trailing comma after their last field. Groovy tolerates it but nf-core's
  linter converts the manifest to JSON and choked (JSONDecodeError). This also
  cascaded into spurious files_exist igenomes failures because the config-aware
  exemption depends on a parseable manifest. Removing the trailing commas clears
  both.
- nf-test: QC processes died with exit status 1 (`Command 'ps' required by
  nextflow to collect task metrics cannot be found`). The micromamba-based QC
  containers lacked procps. Added conda-forge::procps-ng to all three QC
  environment.yml files (source of truth for docker/singularity/conda).

Co-authored-by: Malwina Prater <mprater@altoslabs.com>
Co-authored-by: Nell Nie <nnie@altoslabs.com>
Co-authored-by: Christel Krueger <ckrueger@altoslabs.com>

Author: 4 people

modules/local/image_qc/environment.yml

@@ -4,6 +4,8 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  # procps-ng provides `ps`, required by Nextflow for task-metric collection
+  - conda-forge::procps-ng=4.0.4
   - conda-forge::python=3.11.0
   - conda-forge::numpy=2.3.3
   - conda-forge::pandas=2.3.2

modules/local/quarto/environment.yml

@@ -4,6 +4,8 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  # procps-ng provides `ps`, required by Nextflow for task-metric collection
+  - conda-forge::procps-ng=4.0.4
   - conda-forge::python=3.11.0
   - conda-forge::quarto=1.6.42
   - conda-forge::numpy=2.3.3

modules/local/transcript_qc/environment.yml

@@ -4,6 +4,8 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
+  # procps-ng provides `ps`, required by Nextflow for task-metric collection
+  - conda-forge::procps-ng=4.0.4
   - conda-forge::python=3.11.0
   - conda-forge::numpy=2.3.3
   - conda-forge::pandas=2.3.2

nextflow.config

@@ -409,17 +409,17 @@ manifest {
         [
             name: 'Malwina Prater',
             affiliation: 'Altos Labs',
-            contribution: ['contributor'],
+            contribution: ['contributor']
         ],
         [
             name: 'Nell Nie',
             affiliation: 'Altos Labs',
-            contribution: ['contributor'],
+            contribution: ['contributor']
         ],
         [
             name: 'Christel Krueger',
             affiliation: 'Altos Labs',
-            contribution: ['contributor'],
+            contribution: ['contributor']
         ]
     ]
     homePage        = 'https://github.com/nf-core/spatialaxe'