fixed version in container

AndersenLab · Oct 14, 2024 · 5190ea0 · 5190ea0
1 parent 4d51d3a
commit 5190ea0
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Showing 5 changed files with 18 additions and 12 deletions.
diff --git a/bin/find_stations.R b/bin/find_stations.R
@@ -6,11 +6,11 @@ source(args[6])
 
 library(lubridate)
 #library(tidyverse)
-library(dplyr)
 library(tidyr)
 library(readr)
 library(stationaRy)
 library(geosphere)
+library(dplyr)
 
 # args[1] = input dat#aframe
 # args[2] = station dataframe

diff --git a/env/Dockerfile b/env/Dockerfile
@@ -11,11 +11,13 @@ ARG MAMBA_DOCKERFILE_ACTIVATE=1
 
 USER root
 
-RUN apt-get update && apt-get install -y procps && \
+RUN apt-get update && apt-get install -y procps wget && \
     apt-get clean
 
 USER $MAMBA_USER
 
 ENV PATH=/opt/conda/bin:/opt/conda/condabin:$PATH
 
-RUN Rscript -e "install.packages('stationaRy', dependencies = TRUE, repos = 'http://cran.us.r-project.org')"
+RUN Rscript -e "install.packages('lutz', dependencies = TRUE, repos = 'http://cran.us.r-project.org')"
+RUN wget https://cran.r-project.org/src/contrib/Archive/stationaRy/stationaRy_0.4.1.tar.gz
+RUN Rscript -e "install.packages('stationaRy_0.4.1.tar.gz', repos = NULL, type='source')"
diff --git a/env/conda.yml b/env/conda.yml
@@ -16,4 +16,6 @@ dependencies:
   - r-downloader
   - r-progress
   - r-stringr
-  - r-plyr
+  - r-plyr
+  - r-leaflet
+  - r-magrittr
diff --git a/main.nf b/main.nf
@@ -1,14 +1,15 @@
 #! usr/bin/env nextflow
 
 params.samples = "${workflow.projectDir}/test_data/wild_isolates.csv"
+params.isd_inventory = "${workflow.projectDir}/isd-inventory.csv"
 
 if (params.out == null){
-    params.outdir = noaa_analysis_${date}
+    params.outdir = "noaa_analysis_${params.day}"
 } else {
     params.outdir = params.out
 }
 
-if (params.help){
+if (params.help | params.debug){
     params.input = "${workflow.projectDir}/test_data/noaa_test.csv"
 } else {
     params.input = params.samples
@@ -19,8 +20,9 @@ if (params.help){
 
 workflow {
     Channel.fromPath(params.input) | split_WI
-    split_WI.out.flatten() | findStations
-    findStations.toSortedList() | joinData
+    split_WI.out.flatten()
+        .combine(Channel.of( params.isd_inventory) ) | findStations
+    findStations.out.toSortedList() | joinData
 }
 process split_WI {
   label 'xs'
@@ -79,22 +81,22 @@ process findStations {
   tag { wi_location }
 
   input:
-    path(wi_location)
+    tuple path(wi_location), path(isd_inventory)
 
   output:
     path("*.noaa.tsv")
 
 
   """
-  Rscript --vanilla "${workflow.projectDir}/bin/find_stations.R" "${wi_location}" "${workflow.projectDir}/isd-inventory.csv" "${params.months}" "${params.events}" "${params.important_trait}" "${workflow.projectDir}/bin/get_isd_station_data_fix.R"
+  Rscript --vanilla "${workflow.projectDir}/bin/find_stations.R" "${wi_location}" "${isd_inventory}" "${params.months}" "${params.events}" "${params.important_trait}" "${workflow.projectDir}/bin/get_isd_station_data_fix.R"
 
   """
 
 }
 
 
 process joinData {
-    publishDir "${params.out}/", mode: 'copy'
+    publishDir "${params.outdir}/", mode: 'copy'
 
     executor "local"
     container null

diff --git a/nextflow.config b/nextflow.config
@@ -21,5 +21,5 @@ profiles {
 
 process {
     cache = "lenient"
-    container = "andersenlab/noaa-nf:202410141550086c5701"
+    container = "andersenlab/noaa-nf:101424"
 }