Merge pull request #713 from nf-core/nextflow-duration-fix

Nextflow duration fix

Author: apeltzer

Dockerfile

@@ -1,4 +1,4 @@
-FROM nfcore/base:1.13.2
+FROM nfcore/base:1.13.3
 LABEL authors="The nf-core/eager community" \
       description="Docker image containing all software requirements for the nf-core/eager pipeline"
 

nextflow_schema.json

@@ -305,7 +305,7 @@
                     "description": "Maximum amount of time that can be requested for any single job.",
                     "default": "240.h",
                     "fa_icon": "far fa-clock",
-                    "pattern": "^[\\d\\.]+\\.*(s|m|h|d)$",
+                    "pattern": "^(\\d+(\\.\\d+)?(?:\\s*|\\.?)(s|m|h|d)\\s*)+$",
                     "hidden": true,
                     "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`"
                 }
@@ -609,7 +609,6 @@
                 },
                 "bt2n": {
                     "type": "integer",
-                    "default": 0,
                     "description": "Specify the -N parameter for bowtie2 (mismatches in seed). This will override defaults from alignmode/sensitivity.",
                     "fa_icon": "fas fa-sort-numeric-down",
                     "help_text": "The number of mismatches allowed in the seed during seed-and-extend procedure of Bowtie2. This will override any values set with `--bt2_sensitivity`. Can either be 0 or 1. Default: 0 (i.e. use`--bt2_sensitivity` defaults).\n\n> Modifies Bowtie2 parameters: `-N`",
@@ -620,21 +619,18 @@
                 },
                 "bt2l": {
                     "type": "integer",
-                    "default": 0,
                     "description": "Specify the -L parameter for bowtie2 (length of seed substrings). This will override defaults from alignmode/sensitivity.",
                     "fa_icon": "fas fa-ruler-horizontal",
                     "help_text": "The length of the seed sub-string to use during seeding. This will override any values set with `--bt2_sensitivity`. Default: 0 (i.e. use`--bt2_sensitivity` defaults: [20 for local and 22 for end-to-end](http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml#command-line).\n\n> Modifies Bowtie2 parameters: `-L`"
                 },
                 "bt2_trim5": {
                     "type": "integer",
-                    "default": 0,
                     "description": "Specify number of bases to trim off from 5' (left) end of read before alignment.",
                     "fa_icon": "fas fa-cut",
                     "help_text": "Number of bases to trim at the 5' (left) end of read prior alignment. Maybe useful when left-over sequencing artefacts of in-line barcodes present Default: 0\n\n> Modifies Bowtie2 parameters: `-bt2_trim5`"
                 },
                 "bt2_trim3": {
                     "type": "integer",
-                    "default": 0,
                     "description": "Specify number of bases to trim off from 3' (right) end of read before alignment.",
                     "fa_icon": "fas fa-cut",
                     "help_text": "Number of bases to trim at the 3' (right) end of read prior alignment. Maybe useful when left-over sequencing artefacts of in-line barcodes present Default: 0.\n\n> Modifies Bowtie2 parameters: `-bt2_trim3`"
@@ -685,14 +681,12 @@
                 },
                 "bam_mapping_quality_threshold": {
                     "type": "integer",
-                    "default": 0,
                     "description": "Minimum mapping quality for reads filter.",
                     "fa_icon": "fas fa-greater-than-equal",
                     "help_text": "Specify a mapping quality threshold for mapped reads to be kept for downstream analysis. By default keeps all reads and is therefore set to `0` (basically doesn't filter anything).\n\n> Modifies samtools view parameter: `-q`"
                 },
                 "bam_filter_minreadlength": {
                     "type": "integer",
-                    "default": 0,
                     "fa_icon": "fas fa-ruler-horizontal",
                     "description": "Specify minimum read length to be kept after mapping.",
                     "help_text": "Specify minimum length of mapped reads. This filtering will apply at the same time as mapping quality filtering.\n\nIf used _instead_ of minimum length read filtering at AdapterRemoval, this can be useful to get more realistic endogenous DNA percentages, when most of your reads are very short (e.g. in single-stranded libraries) and would otherwise be discarded by AdapterRemoval (thus making an artificially small denominator for a typical endogenous DNA calculation). Note in this context you should not perform mapping quality filtering nor discarding of unmapped reads to ensure a correct denominator of all reads, for the endogenous DNA calculation.\n\n> Modifies filter_bam_fragment_length.py parameter: `-l`"
@@ -1051,7 +1045,6 @@
                 },
                 "freebayes_g": {
                     "type": "integer",
-                    "default": 0,
                     "description": "Specify to skip over regions of high depth by discarding alignments overlapping positions where total read depth is greater than specified in --freebayes_C.",
                     "fa_icon": "fab fa-think-peaks",
                     "help_text": "Specify to skip over regions of high depth by discarding alignments overlapping positions where total read depth is greater than specified C. Not set by default.\n\n> Modifies freebayes parameter: `-g`"
@@ -1643,4 +1636,4 @@
             "$ref": "#/definitions/metagenomic_authentication"
         }
     ]
-}
+}