bug fixes for CAMPneu

recipes/CAMPneu/build.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+# $PYTHON -m pip install . -vv
+
+mkdir -p $PREFIX/bin/
+
+cp CAMPneu.nf nextflow.config $PREFIX/bin/
+
+chmod +x $PREFIX/bin/CAMPneu.nf $PREFIX/bin/nextflow.config

recipes/CAMPneu/meta.yaml

@@ -0,0 +1,59 @@
+{% set name = "CAMPneu" %}
+{% set version = "1.1.1" %}
+{% set hash = "1fab075c22e8f70c5677fa845018c2dcb489f7c540e14a553f0f387fe7d0f91c" %}
+{% set user = "appliedbinf" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/{{ user }}/{{ name }}/archive/refs/tags/{{ version }}.tar.gz
+  sha256: {{ hash }}
+
+build:
+  number: 0
+  noarch: generic
+  script:
+    - mkdir -p $PREFIX/bin/
+    - cp CAMPneu.nf nextflow.config $PREFIX/bin/
+    - chmod +x $PREFIX/bin/CAMPneu.nf $PREFIX/bin/nextflow.config
+
+  run_exports:
+    - {{ pin_subpackage(name, max_pin='x') }}
+
+requirements:
+  build:
+    - python
+    - setuptools
+    - skip: True  # [win]
+
+  host:
+    - python
+    - pip
+
+  run:
+    - nextflow
+    - python <3.11
+    - minimap2==2.28
+    - samtools
+    - fastp
+    - fastANI
+    - bcftools
+    - kraken2
+    - unicycler
+    - freebayes
+    - jq
+
+test:
+  commands:
+    - CAMPneu.nf --help
+
+about:
+  home: "https://github.com/{{ user }}/{{ name }}"
+  license: MIT
+  license_family: MIT
+  license_file: LICENSE
+  summary: "CAMPneu is a scalable and reproducible Nextflow pipeline designed for bioinformatics analysis, targeting Illumina paired-end sequence data. Its primary objectives are to identify Mycoplasma pneumoniae species, classify its subtype (type 1 or type 2), and detect known SNPs associated with macrolide resistance in the sample."
+  dev_url: "https://github.com/{{ user }}/{{ name }}"
+  doc_url: "https://github.com/appliedbinf/campneu/blob/{{ version }}/README.md"