Merge pull request #26 from evotools/v184

v1.8.4
evotools · Nov 16, 2024 · f208a3a · f208a3a
2 parents e461f41 + 370029b
commit f208a3a
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Showing 11 changed files with 56 additions and 29 deletions.
diff --git a/.github/workflows/CI-mm2.yml b/.github/workflows/CI-mm2.yml
@@ -49,4 +49,4 @@ jobs:
       - name: Run pipeline with test data and minimap2
         run: |
           source ./mambaforge/etc/profile.d/conda.sh
-          nextflow run ${GITHUB_WORKSPACE} --aligner minimap2 --mamba -profile test,conda
+          nextflow run ${GITHUB_WORKSPACE} --aligner minimap2 --report --mamba -profile test,conda
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,9 @@
 # Changelog
+## [v1.8.4]
+- Fix broken anaconda environment creation due to wrong repository order 
+- Better schema file
+- Report generation is now optional and enabled with `--report`
+- Report now working with anaconda runs
 
 ## [v1.8.3]
 - Added `--haplotypes` mode, that allows to create liftover files between haplotypes of the same individual with UCSC naming convention 

diff --git a/assets/environment.yml b/assets/environment.yml
@@ -1,7 +1,7 @@
 name: nf-LO
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - defaults
 dependencies:
   - bedtools=2.30.0

diff --git a/assets/maf-environment.yml b/assets/maf-environment.yml
@@ -1,7 +1,7 @@
 name: nf-LO-r
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - defaults
 dependencies:
   - genomedk::maftools
diff --git a/assets/r-environment.yml b/assets/r-environment.yml
@@ -1,7 +1,7 @@
 name: nf-LO-r
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - defaults
 dependencies:
   - xorg-libxau=1.0.9

diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,4 +1,10 @@
 # Changelog
+## [v1.8.4]
+- Fix broken anaconda environment creation due to wrong repository order 
+- Better schema file
+- Report generation is now optional and enabled with `--report`
+- Report now working with anaconda runs
+
 ## [v1.8.3]
 - Added `--haplotypes` mode, that allows to create liftover files between haplotypes of the same individual with UCSC naming convention 
 

diff --git a/environment.yml b/environment.yml
@@ -1,7 +1,7 @@
 name: nf-LO
 channels:
-  - bioconda
   - conda-forge
+  - bioconda
   - defaults
 dependencies:
   - bedtools=2.31.0

diff --git a/main.nf b/main.nf
@@ -70,6 +70,7 @@ annot type      : $params.annotation_format
 liftover meth.  : $params.liftover_algorithm
 igenomes_base   : $params.igenomes_base
 igenomes_ignore : $params.igenomes_ignore
+report          : $params.report
 mamba           : $params.mamba
 no_maf          : $params.no_maf"""
 if (params.qscores){
@@ -131,7 +132,7 @@ workflow {
         } else {
                 liftstats = file("${params.outdir}/stats/placeholder4")
         }
-        if (params.mafTools || params.annotation || workflow.containerEngine){
+        if (params.report){
                 rmd = Channel.fromPath("${baseDir}/assets/gatherMetrics.Rmd")
                 make_report(ALIGNER.out.mafs, ALIGNER.out.mafc, ALIGNER.out.mafi, liftstats, rmd)
         }

diff --git a/modules/processes/postprocess.nf b/modules/processes/postprocess.nf
@@ -424,6 +424,7 @@ process features_stats {
     tag "feat_stats"
     publishDir "${params.outdir}/stats", mode: params.publish_dir_mode, overwrite: true
     label 'medium'
+    conda "${baseDir}/assets/maf-environment.yml"
 
     input:
         path all_feature

diff --git a/nextflow.config b/nextflow.config
@@ -23,7 +23,7 @@ params {
     tgtOvlp = 100000
     srcOvlp = 0
     qscores = null
-    outdir = "${launchDir}/OUTPUTS" 
+    outdir = "${launchDir}/OUTPUTS"
     annotation = null
     annotation_format = null
     custom = null
@@ -36,6 +36,7 @@ params {
     no_maf = false
     no_netsynt = false
     mafTools = null
+    report = false
     reciprocal_best = false
     mm2_full_alignment = false
     mm2_lowmem = false
@@ -104,6 +105,7 @@ profiles {
     conda.useMamba = params.mamba ? true : false
   }
   docker {
+    process.container = "nflo:latest"
     docker.enabled         = true
     docker.userEmulation   = true
     singularity.enabled    = false
@@ -112,6 +114,7 @@ profiles {
     charliecloud.enabled   = false
   }
   singularity {
+    process.container = "docker-daemon://nflo:latest"
     singularity.enabled    = true
     singularity.autoMounts = true
     docker.enabled         = false
@@ -190,7 +193,7 @@ manifest {
   mainScript      = 'main.nf'
   nextflowVersion = '>=21.10.0'
   defaultBranch   = 'main'
-  version         = '1.8.3'
+  version         = '1.8.4'
 }
 
 

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -22,31 +22,36 @@
                 },
                 "source": {
                     "type": "string",
-                    "default": "null"
+                    "format": "file-path"
                 },
                 "target": {
                     "type": "string",
-                    "default": "null"
+                    "format": "file-path"
                 },
                 "ncbi_source": {
                     "type": "boolean",
-                    "default": "false"
+                    "default": false
                 },
                 "ncbi_target": {
                     "type": "boolean",
-                    "default": "false"
+                    "default": false
                 },
                 "igenomes_source": {
                     "type": "boolean",
-                    "default": "false"
+                    "default": false
                 },
                 "igenomes_target": {
                     "type": "boolean",
-                    "default": "false"
+                    "default": false
+                },
+                "report": {
+                    "type": "boolean",
+                    "default": false,
+                    "description": "Save HTML report."
                 },
                 "annotation": {
                     "type": "string",
-                    "default": "null"
+                    "format": "file-path"
                 },
                 "annotation_format": {
                     "type": "string",
@@ -77,27 +82,32 @@
                 },
                 "srcSize": {
                     "type": "integer",
-                    "default": 20000000
+                    "default": 20000000,
+                    "description": "Chunk size of the source genome for the alignment" 
                 },
-                "tgtSize": {
+                "srcOvlp": {
                     "type": "integer",
-                    "default": 10000000
+                    "default": 0,
+                    "description": "Overlap size between chunks of the source genome"
                 },
-                "tgtOvlp": {
+                "tgtSize": {
                     "type": "integer",
-                    "default": 100000
+                    "default": 10000000,
+                    "description": "Chunk size of the target genome for the alignment"
                 },
-                "srcOvlp": {
+                "tgtOvlp": {
                     "type": "integer",
-                    "default": 0
+                    "default": 100000,
+                    "description": "Overlap size between chunks of the target genome"
                 },
                 "qscores": {
                     "type": "string",
-                    "default": "null"
+                    "format": "file-path",
+                    "description": "Path to the Q-scores to be used by the `lastz` alignment"
                 },
                 "custom": {
                     "type": "string",
-                    "default": "null"
+                    "description": "Alignment custom options"
                 }
             }
         },
@@ -109,15 +119,15 @@
             "properties": {
                 "chainCustom": {
                     "type": "string",
-                    "default": "null"
+                    "description": "Chaining custom options"
                 },
                 "chain_name": {
                     "type": "string",
                     "default": "liftover"
                 },
                 "no_netsynt": {
                     "type": "boolean",
-                    "default": "false"
+                    "default": false
                 }        
             }
         },
@@ -146,11 +156,12 @@
                 },
                 "no_maf": {
                     "type": "boolean",
-                    "default": "false"
+                    "default": false
                 },
                 "mafTools": {
                     "type": "string",
-                    "default": "null"
+                    "format": "directory-path",
+                    "description": "Path to the installation directory of mafTools"
                 }
             }
         },
@@ -252,7 +263,7 @@
                 "mamba": {
                     "description": "Use mamba instead of conda to create the anaconda environment.",
                     "type": "boolean",
-                    "default": "false"
+                    "default": false
                 },
                 "extra_cluster_options": {
                     "description": "Additional cluster options to be used; valid in some clusters only.",