added documentation to script

tiagofilipe12 · Feb 5, 2018 · 3058a16 · 3058a16
1 parent 90c4411
commit 3058a16
Show file tree

Hide file tree

Showing 4 changed files with 38 additions and 34 deletions.
diff --git a/README.md b/README.md
@@ -11,26 +11,34 @@ It will output a `JSON` file that can be imported into [pATLAS](http://www.patla
 ## Usage
 
 ```
---threads       Number of threads that mash screen will have to run.   
-    Default: 1
---kMer      the length of the kmer to be used by mash.   Default: 21
---pValue        The p-value cutoff. Default: 0.05
---identity      The minimum identity value between two sequences. Default: 0.9
---noWinner      This option allows to disable the -w option of mash screen  
-    Default: false
---refSketch     The file that has the reference mash screen usedby pATLAS  
-    Default: reference/patlas.msh
---reads     The path to the read files. Here users may provide many samples in 
-    the same directory. However be assured that glob pattern is unique 
-    (e.g. 'path/to/*_{1,2}.fastq'). Default: reads/*_{1,2}.fastq.gz
---singleEnd     Provide this option if you have single-end reads. By default 
-    the pipeline will assume that you provide paired-end reads.    Default: false
---help      Opens this help. It will open only when --help is provided. So, 
-    yes, this line is pretty useless since you already know that if you 
-    reached here.
+Usage:
+   nextflow run tiagofilipe12/pATLAS_mash_screen.nf
+
+   Nextflow magic options:
+       -profile    Forces nextflow to run with docker or singularity.   Default: docker     Choices: standard, singularity
+   Main options:
+       --help  Opens this help. It will open only when --help is provided. So, yes, this line is pretty useless since you already know that if you reached here.
+       --version   Prints the version of the pipeline script.
+       --threads   Number of threads that mash screen will have to run.    Default: 1
+       --mash_screen   Enables mash screen run.
+       --assembly  Enables mash dist run to use fasta file against plasmid db
+       --mapping   Enables mapping pipeline.
+   Mash options:
+       --kMer  the length of the kmer to be used by mash.   Default: 21
+       --pValue    The p-value cutoff. Default: 0.05
+   Mash screen exclusive options:
+       --identity  The minimum identity value between two sequences. Default: 0.9
+       --noWinner  This option allows to disable the -w option of mash screen  Default: false
+   Mash dist exclusive options:
+       --mash_distance     Provide the maximum distance between two plasmids to be reported.   Default: 0.1
+   Reads options:
+       --reads The path to the read files. Here users may provide many samples in the same directory. However be assured that glob pattern is unique (e.g. 'path/to/*_{1,2}.fastq').
+       --singleEnd Provide this option if you have single-end reads. By default the pipeline will assume that you provide paired-end reads.    Default: false
+    Fasta options:
+       --fasta     Provide fasta file pattern to be searched by nextflow.  Default: 'fasta/*.fas'
 ```
 
-## TODO
 
-* Default inputs for `reads` and `refSketch` are still sketchy and `patlas.msh`
-should be downloaded [here](https://github.com/tiagofilipe12/mash_wrapper/releases/download/1.0.5/patlas.msh) for now.
+## Example run
+
+`nextflow run tiagofilipe12/pATLAS_auxiliary_scripts --assembly`
diff --git a/lib/Helper.groovy b/lib/Helper.groovy
@@ -8,6 +8,9 @@ class Help{
         println("===========================================================\n")
         println("Usage:")
         println("   nextflow run tiagofilipe12/pATLAS_mash_screen.nf\n")
+        println("   Nextflow magic options:")
+        println("       -profile    Forces nextflow to run with docker or " +
+            "singularity.   Default: docker     Choices: standard, singularity")
         println("   Main options:")
         println("       --help  Opens this help. It will open only when --help is " +
             "provided. So, yes, this line is pretty useless since you already " +
@@ -22,8 +25,6 @@ class Help{
         println("   Mash options:")
         println("       --kMer  the length of the kmer to be used by mash.   Default: 21")
         println("       --pValue    The p-value cutoff. Default: 0.05")
-        println("       --refSketch The file that has the reference mash screen used" +
-            " by pATLAS  Default: reference/patlas.msh")
         println("   Mash screen exclusive options:")
         println("       --identity  The minimum identity value between two sequences." +
             " Default: 0.9")

diff --git a/nextflow.config b/nextflow.config
@@ -37,16 +37,16 @@ process {
 
 // this should be passed with the -profile mash_screen
 profiles {
-    // standard uses executor local and docker
+//    // standard uses executor local and docker
     standard {
         docker.enabled = true
     }
     singularity {
         singularity.enabled = true
-        process.$mashScreen.container = 'docker://tiagofilipe12/patlas_mash_screen:latest'
-        process.$mashOutputJson.container = 'docker://tiagofilipe12/patlas_mash_screen:latest'
-        process.$runMashDist.container = 'docker://tiagofilipe12/patlas_mash_screen:latest'
-        process.$mashDistOutputJson.container = 'docker://tiagofilipe12/patlas_mash_screen:latest'
+//        process.$mashScreen.container = 'docker://tiagofilipe12/patlas_mash_screen:latest'
+//        process.$mashOutputJson.container = 'docker://tiagofilipe12/patlas_mash_screen:latest'
+//        process.$runMashDist.container = 'docker://tiagofilipe12/patlas_mash_screen:latest'
+//        process.$mashDistOutputJson.container = 'docker://tiagofilipe12/patlas_mash_screen:latest'
     }
-    // TODO make a profile for slurm
+//    // TODO make a profile for slurm
 }
diff --git a/pATLAS_mash_screen.nf b/pATLAS_mash_screen.nf
@@ -13,7 +13,7 @@ if (params.help) {
 winnerVar = (params.noWinner == false) ? "-w" : ""
 
 // start all optional channels
-readInputs = readInputs2 = mashRef = mashRef2 = fastaInputs = Channel.empty()
+readInputs = readInputs2 = fastaInputs = Channel.empty()
 
 /**
 * The combination of these four channels (two forked) allows to double check for
@@ -28,9 +28,6 @@ if (params.mash_screen || params.mapping) {
 }
 if (params.mash_screen || params.assembly) {
     refSketch = "/home/data/patlas.msh"
-//    Channel.fromPath("/home/data/*.msh")
-//        .ifEmpty { exit 0, "no mash sketch"}
-//        .into { mashRef; mashRef2 }
 }
 
 /**
@@ -65,7 +62,6 @@ process mashScreen {
 
     input:
     set sample, file(reads) from readInputs
-//    file db from mashRef
 
     output:
     file "sortedMashScreenResults_${sample}.txt" into mashScreenResults
@@ -100,7 +96,6 @@ process runMashDist {
 
     input:
     file fasta from fastaInputs
-//    file db from mashRef2
 
     output:
     file "${fasta}_mashdist.txt" into mashDistResults