Pipeline breaking when I tried to run with -r 2.1.1 instead of -r dev

[AASTHAPAL9]

Description of the bug

Hi,

I am not sure if this any compatibility issue but I couldn't run the pipeline with -r 2.1.1 which was suggested by one of the nfcore crisprseq developer. However when I did get something using -r dev it failed at some other step. I haven't been able to traceback the error and would appreciate any help in debugging.

Command used and terminal output

nextflow run nf-core/crisprseq -r 2.1.1 --input samplesheet_w_control.csv --mle_design_matrix design_matrix.txt --library final_input_sgrna.tsv --analysis screening --outdir /home/ap764/mageck/output -profile conda

Relevant files

The error when I ran the same command with -r dev :

`executor > local (8)
[90/f186a3] NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:FASTQC (POST-KCNM-CDR-O) | 5 of 5 ✔
[ad/da22ac] NFC…R-O,PRE-CDR-O,POST-EGF-CDR-O,POST-KCNM-CDR-O,POST-PTPRZ-CDR-O) | 1 of 1 ✔
[7b/c72af1] NFC…RISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_MLE_MATRIX (design_matrix) | 1 of 1 ✔
[8d/013eae] NFC…_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE (design_matrix) | 1 of 1, failed: 1 ✘
[- ] NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MULTIQC -
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/crisprseq] Pipeline completed with errors-
ERROR ~ Error executing process > 'NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE (design_matrix)'

Caused by:
Process NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE (design_matrix) terminated with an error exit status (127)

Command executed [/home/ap764/.nextflow/assets/nf-core/crisprseq/templates/template_fluteMLE.R]:

#!/usr/bin/env Rscript

author: Laurence Kuhlburger

Released under the MIT license. See git repository (https://github.com/nf-core/crisprseq) for full license text.

graphs mageck MLE

library(MAGeCKFlute)
library(clusterProfiler)
library(ggplot2)

library(pathview)
options(ggrepel.max.overlaps = Inf)
mle <- read.table("design_matrix.gene_summary.txt", header = TRUE, sep = " ", stringsAsFactors = FALSE)

if("design_matrix" == "day0") {
beta_strings <- grep("\.beta", colnames(mle), value = TRUE)
before_beta <- sub("\.beta.", "", beta_strings)
unique_strings <- unique(before_beta)
for(i in unique_strings) {
tryCatch(
{
FluteMLE(mle, treatname= i, proj=i, pathview.top=5)
},
error=function(e) {
print(paste("Could not run FluteMLE with project",i))
}
)
}
} else {
beta_strings <- grep("\.beta", colnames(mle), value = TRUE)
before_beta <- sub("\.beta.", "", beta_strings)
unique_strings <- unique(before_beta)
for(i in unique_strings) {
tryCatch(
{
FluteMLE(mle, treatname= i, proj=i, , pathview.top=5)
},
error=function(e) {
print(paste("Could not run FluteMLE with project",i))
}
)
}
}

version_file_path <- "versions.yml"
version_flute <- paste(unlist(packageVersion("MAGeCKFlute")), collapse = ".")
version_ggplot <- paste(unlist(packageVersion("ggplot2")), collapse = ".")
version_clusterprofiler <- paste(unlist(packageVersion("clusterProfiler")), collapse = ".")
version_pathview <- paste(unlist(packageVersion("pathview")), collapse = ".")

f <- file(version_file_path, "w")
writeLines('"NFCORE_CRISPRSEQ:CRISPRSEQ_SCREENING:MAGECK_FLUTEMLE":', f)
writeLines(" MAGeCKFlute: ", f, sep = "")
writeLines(version_flute, f)
writeLines(" ggplot2: ", f, sep = "")
writeLines(version_ggplot, f)
writeLines(" clusterProfiler: ", f, sep = "")
writeLines(version_clusterprofiler, f)
writeLines(" pathview: ", f, sep = "")
writeLines(version_pathview, f)
close(f)

Command exit status:
127

Command output:
(empty)

Command error:
/usr/bin/env: 'Rscript': No such file or directory

Work dir:
/home/ap764/mageck/work/8d/013eae9d1032316baef01978a208a4

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details`

System information

No response

[LaurenceKuhl]

Hi @AASTHAPAL9
sorry for getting back to you so late! Is there any chance you could run it with docker instead of conda? We're experiencing some difficulties:

nextflow run nf-core/crisprseq -r 2.1.1 --input samplesheet_w_control.csv --mle_design_matrix design_matrix.txt --library final_input_sgrna.tsv --analysis screening --outdir /home/ap764/mageck/output -profile docker

let me know if this is possible :)