Fixed nf-core lint warnings

.github/workflows/awsfulltest.yml

@@ -15,7 +15,6 @@ jobs:
     steps:
       - name: Launch workflow via tower
         uses: seqeralabs/action-tower-launch@v2
-        # TODO nf-core: You can customise AWS full pipeline tests as required
         # Add full size test data (but still relatively small datasets for few samples)
         # on the `test_full.config` test runs with only one set of parameters
         with:

.github/workflows/ci.yml

@@ -36,7 +36,6 @@ jobs:
           version: "${{ matrix.NXF_VER }}"
 
       - name: Run pipeline with test data
-        # TODO nf-core: You can customise CI pipeline run tests as required
         # For example: adding multiple test runs with different parameters
         # Remember that you can parallelise this by using strategy.matrix
         run: |

.nf-core.yml

@@ -2,4 +2,7 @@ repository_type: pipeline
 template:
   prefix: nf-core
   skip:
-  - igenomes
+    - igenomes
+lint:
+  files_exist:
+    - conf/igenomes.config

conf/base.config

@@ -23,7 +23,6 @@ process {
     //        These labels are used and recognised by default in DSL2 files hosted on nf-core/modules.
     //        If possible, it would be nice to keep the same label naming convention when
     //        adding in your local modules too.
-    // TODO nf-core: Customise requirements for specific processes.
     // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
     withLabel:process_single {
         cpus   = { check_max( 1                  , 'cpus'    ) }

conf/modules.config

@@ -124,7 +124,7 @@ process {
         publishDir = [
             path:    "${params.outdir}/trend/mosaic/",
             mode:    params.publish_dir_mode,
-            saveAs:  { it -> it.equals('versions.yml') ? null : "${params.outdir}/trend/mosaic/${task.tag}/${it.replaceAll("trend/","")}"}
+            saveAs:  { it.equals('versions.yml') ? null : "${params.outdir}/trend/mosaic/${task.tag}/${it.replaceAll("trend/","")}"}
         ]
     }
 

modules/local/check_results.nf

@@ -2,6 +2,8 @@ nextflow.enable.dsl = 2
 
 process CHECK_RESULTS {
 
+    label 'process_low'
+
     container 'docker.io/rocker/geospatial:4.3.1'
 
     input:
@@ -16,6 +18,9 @@ process CHECK_RESULTS {
     output:
     path "versions.yml" , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     files=`find ./trend/ -maxdepth 1 -mindepth 1 -type d`

modules/local/force-generate_analysis_mask.nf

@@ -2,6 +2,8 @@ nextflow.enable.dsl = 2
 
 process FORCE_GENERATE_ANALYSIS_MASK{
 
+    label 'process_single'
+
     container "docker.io/davidfrantz/force:3.7.11"
 
     input:
@@ -13,6 +15,9 @@ process FORCE_GENERATE_ANALYSIS_MASK{
     path 'mask/*/*.tif', emit: masks
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     force-cube -o mask/ -s $params.resolution $aoi

modules/local/force-generate_tile_allow_list.nf

@@ -2,6 +2,8 @@ nextflow.enable.dsl = 2
 
 process FORCE_GENERATE_TILE_ALLOW_LIST{
 
+    label 'process_single'
+
     container "docker.io/davidfrantz/force:3.7.11"
 
     input:
@@ -13,6 +15,9 @@ process FORCE_GENERATE_TILE_ALLOW_LIST{
     path 'tile_allow.txt', emit: tile_allow
     path "versions.yml"  , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     force-tile-extent $aoi tmp/ tile_allow.txt

modules/local/force-higher_level.nf

@@ -2,16 +2,21 @@ nextflow.enable.dsl = 2
 
 process FORCE_HIGHER_LEVEL {
 
+    label 'process_high'
+
     container "docker.io/davidfrantz/force:3.7.11"
-    tag {tile}
+    tag { tile }
 
     input:
-    tuple val(tile), path( config ), path( ard ), path( aoi ), path ( datacube ), path ( endmember )
+    tuple val(tile), path(config), path(ard), path(aoi), path (datacube), path (endmember)
 
     output:
     path 'trend/*.tif*', emit: trend_files
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     PARAM=$config

modules/local/force-mosaic.nf

@@ -2,16 +2,21 @@ nextflow.enable.dsl = 2
 
 process FORCE_MOSAIC{
 
+    label 'process_low'
+
     tag { product }
     container "docker.io/davidfrantz/force:3.7.11"
 
     input:
-    tuple val( product ), path('trend/*')
+    tuple val(product), path('trend/*')
     path 'trend/datacube-definition.prj'
 
     output:
-    tuple val( product ), path( 'trend/*' ), emit: trend_files
-    path "versions.yml"                    , emit: versions
+    tuple val(product), path('trend/*'), emit: trend_files
+    path "versions.yml"                , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
 
     script:
     """

modules/local/force-preprocess.nf

@@ -1,6 +1,8 @@
 nextflow.enable.dsl=2
 
 process FORCE_PREPROCESS {
+
+    label 'process_medium'
     tag { data.simpleName }
 
     container "docker.io/davidfrantz/force:3.7.11"
@@ -11,9 +13,12 @@ process FORCE_PREPROCESS {
     output:
     path "**/*BOA.tif", optional:true, emit: boa_tiles
     path "**/*QAI.tif", optional:true, emit: qai_tiles
-    path "*.log"
+    path "*.log"                     , emit: log
     path "versions.yml"              , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     PARAM=$conf

modules/local/force-pyramid.nf

@@ -2,16 +2,21 @@ nextflow.enable.dsl = 2
 
 process FORCE_PYRAMID {
 
+    label 'process_low'
     tag { tile }
+
     container "docker.io/davidfrantz/force:3.7.11"
 
     input:
-    tuple val( tile ), path( image )
+    tuple val(tile), path(image)
 
     output:
-    path( '**' ),        emit: trends
+    path('**')         , emit: trends
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     files="*.tif"

modules/local/higher_level_force_config.nf

@@ -2,18 +2,23 @@ nextflow.enable.dsl = 2
 
 process HIGHER_LEVEL_CONFIG {
 
-    container "docker.io/davidfrantz/force:3.7.11"
+    label 'process_single'
     tag { tile }
 
+    container "docker.io/davidfrantz/force:3.7.11"
+
     input:
-    tuple val( tile ), path( "ard/${tile}/*" ), path( "ard/${tile}/*" ), path( "mask/${tile}/aoi.tif" )
+    tuple val(tile), path("ard/${tile}/*"), path("ard/${tile}/*"), path("mask/${tile}/aoi.tif")
     path 'ard/datacube-definition.prj'
     path endmember
 
     output:
-    tuple val (tile), path( "trend_${tile}.prm" ), path( "ard/", includeInputs: true  ), path( "mask/", includeInputs: true ), path( 'ard/datacube-definition.prj', includeInputs: true ), path( endmember, includeInputs: true ), emit: higher_level_configs_and_data
+    tuple val (tile), path("trend_${tile}.prm"), path("ard/", includeInputs: true), path("mask/", includeInputs: true), path('ard/datacube-definition.prj', includeInputs: true), path(endmember, includeInputs: true), emit: higher_level_configs_and_data
     path "versions.yml", emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     # generate parameterfile from scratch

modules/local/merge.nf

@@ -2,19 +2,23 @@ nextflow.enable.dsl = 2
 
 process MERGE {
 
+    label 'process_low'
     tag { id }
 
     container 'docker.io/davidfrantz/force:dev'
 
     input:
-    val ( data_type ) // defines whether qai or boa is merged
-    tuple val( id ), path( 'input/?/*' )
+    val (data_type) // defines whether qai or boa is merged
+    tuple val(id), path('input/?/*')
     path cube
 
     output:
-    tuple val( id ), path( "*.tif" ), emit: tiles_merged
+    tuple val(id), path("*.tif"), emit: tiles_merged
     path "versions.yml"             , emit: versions
 
+    when:
+    task.ext.when == null || task.ext.when
+
     script:
     """
     files=`find -L input/ -type f -printf "%f\\n" | sort | uniq`

modules/local/preprocess_force_config.nf

@@ -2,6 +2,7 @@ nextflow.enable.dsl = 2
 
 process PREPROCESS_CONFIG {
 
+    label 'process_single'
     tag { data.simpleName }
 
     container "docker.io/davidfrantz/force:3.7.11"
@@ -14,9 +15,11 @@ process PREPROCESS_CONFIG {
     path wvdb
 
     output:
-    tuple path("*.prm"), path(data), path(cube), path(tile), path(dem), path(wvdb),  emit: preprocess_config_and_data
-    path "*.prm"
-    path "versions.yml", emit: versions
+    tuple path("*.prm"), path(data), path(cube), path(tile), path(dem), path(wvdb), emit: preprocess_config_and_data
+    path "versions.yml"                                                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
 
     script:
     """

nextflow_schema.json

@@ -14,10 +14,10 @@
             "properties": {
                 "input": {
                     "type": "string",
-                    "default": "None",
                     "fa_icon": "fas fa-satellite",
                     "help_text": "Set this to the root directory of all satellite imagery. Directory structure should match format of data downloaded with '$ force-level1-csd\n' For concrete directory structure see ./docs/usage.md ",
-                    "description": "Root directory of all sattelite imagery."
+                    "description": "Root directory of all sattelite imagery.",
+                    "mimetype": "application/x-tar"
                 },
                 "input_tar": {
                     "type": "boolean",
@@ -27,7 +27,6 @@
                 },
                 "dem": {
                     "type": "string",
-                    "default": "None",
                     "help_text": "Path to directory containing a subdirectory with tile-wise digital elevation files (.tif) and a virtual dataset file (.vrt file) comprising all tile-wise files from the subdirectory.  \n\n\n",
                     "fa_icon": "fas fa-mountain",
                     "description": "Digital elevation model."
@@ -40,7 +39,6 @@
                 },
                 "wvdb": {
                     "type": "string",
-                    "default": "None",
                     "fa_icon": "fas fa-burn",
                     "description": "Water vapor dataset.",
                     "help_text": "Directory containg a number text files describing global water vapor data at different timestamps, and a coordinate order (.coo-)file containig the reference system of the water vapor data."
@@ -53,21 +51,18 @@
                 },
                 "data_cube": {
                     "type": "string",
-                    "default": "None",
                     "description": "Datacube definition.",
                     "fa_icon": "fas fa-cube",
                     "help_text": "A single .prj file describing the projection and reference grid of the generated datacube."
                 },
                 "aoi": {
                     "type": "string",
-                    "default": "None",
                     "fa_icon": "fas fa-chart-area",
                     "description": "Area of interest.",
                     "help_text": "A single vector file specifying the spacial extend of the targeted area."
                 },
                 "endmember": {
                     "type": "string",
-                    "default": "None",
                     "fa_icon": "fas fa-chart-line",
                     "description": "Endmember definition.",
                     "help_text": "A single text file specifying where lines correspond to satellite bands and columns correspond to endmembers. Values correspond to reflectance values and are separated by spaces."