From effde36dee924acd39d5b6e7a40a7f13335908a9 Mon Sep 17 00:00:00 2001
From: Dominik Brilhaus <brilhaus@nfdi4plants.org>
Date: Fri, 14 Mar 2025 13:58:02 +0100
Subject: [PATCH] try fix kallisto_vollect (fails due to docker deps)

---
 runs/kallisto_collect/README.md               |     6 -
 runs/kallisto_collect/out/isa.dataset.xlsx    |   Bin 13276 -> 0 bytes
 .../out/kallisto_mappingStats.csv             |     7 -
 .../out/kallisto_sleuthObject.RData           |     3 -
 .../out/kallisto_tpmMatrix.csv                | 31435 ----------------
 runs/kallisto_collect/run.cwl                 |    27 +
 runs/kallisto_collect/run.yml                 |     2 +-
 workflows/deseq2/deseq2.R                     |     4 +-
 workflows/kallisto_collect/Dockerfile         |    29 +
 workflows/kallisto_collect/kallisto_collect.R |    28 +-
 .../kallisto_collect/kallisto_collect.cwl     |    46 -
 workflows/kallisto_collect/workflow.cwl       |    52 +
 12 files changed, 120 insertions(+), 31519 deletions(-)
 delete mode 100644 runs/kallisto_collect/README.md
 delete mode 100644 runs/kallisto_collect/out/isa.dataset.xlsx
 delete mode 100644 runs/kallisto_collect/out/kallisto_mappingStats.csv
 delete mode 100644 runs/kallisto_collect/out/kallisto_sleuthObject.RData
 delete mode 100644 runs/kallisto_collect/out/kallisto_tpmMatrix.csv
 create mode 100644 runs/kallisto_collect/run.cwl
 create mode 100644 workflows/kallisto_collect/Dockerfile
 delete mode 100644 workflows/kallisto_collect/kallisto_collect.cwl
 create mode 100644 workflows/kallisto_collect/workflow.cwl

diff --git a/runs/kallisto_collect/README.md b/runs/kallisto_collect/README.md
deleted file mode 100644
index a680462..0000000
--- a/runs/kallisto_collect/README.md
+++ /dev/null
@@ -1,6 +0,0 @@
-
-
-```bash
-cd runs/kallisto_collect/
-cwltool ../../workflows/kallisto_collect/kallisto_collect.cwl run.yml > $(date +"%Y-%m-%d_%H-%M").log 2>&1 &
-```
diff --git a/runs/kallisto_collect/out/isa.dataset.xlsx b/runs/kallisto_collect/out/isa.dataset.xlsx
deleted file mode 100644
index f590d99f95e7568392f316133577e385bd72228b..0000000000000000000000000000000000000000
GIT binary patch
literal 0
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diff --git a/runs/kallisto_collect/out/kallisto_mappingStats.csv b/runs/kallisto_collect/out/kallisto_mappingStats.csv
deleted file mode 100644
index 21b8d2b..0000000
--- a/runs/kallisto_collect/out/kallisto_mappingStats.csv
+++ /dev/null
@@ -1,7 +0,0 @@
-"ID","n_targets","n_bootstraps","n_processed","n_pseudoaligned","n_unique","p_pseudoaligned","p_unique","kallisto_version","index_version","start_time","call"
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-"DB_099",31434,100,14332278,10066506,9848811,70.2,68.7,"0.44.0",10,"Fri Aug  6 15:49:19 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_099 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_099_CAMMD_CTTGTA_L001_R1_001.fastq.gz"
-"DB_103",31434,100,13083957,9007720,8828236,68.8,67.5,"0.44.0",10,"Fri Aug  6 15:50:41 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_103 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_103_CAMMD_AGTCAA_L001_R1_001.fastq.gz"
-"DB_161",31434,100,12785081,9058396,8740183,70.9,68.4,"0.44.0",10,"Fri Aug  6 15:51:58 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_161 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_161_reC3MD_GTCCGC_L001_R1_001.fastq.gz"
-"DB_163",31434,100,14312514,10054493,9707941,70.2,67.8,"0.44.0",10,"Fri Aug  6 15:53:12 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_163 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_163_reC3MD_GTGAAA_L001_R1_001.fastq.gz"
-"DB_165",31434,100,13679479,9552504,9264346,69.8,67.7,"0.44.0",10,"Fri Aug  6 15:54:35 2021","kallisto quant --single -b 100 -t 30 -l 200 -s 20 -i /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_index -o /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005//runs/01_kallisto_results/DB_165 /Users/dominikbrilhaus/sciebo/CEPLAS_DM/CEPLAS_ARCs/ARC0005/assays/Talinum_RNASeq_minimal/dataset/DB_165_re-C3MD_GTGAAA_L002_R1_001.fastq.gz"
diff --git a/runs/kallisto_collect/out/kallisto_sleuthObject.RData b/runs/kallisto_collect/out/kallisto_sleuthObject.RData
deleted file mode 100644
index 01ae821..0000000
--- a/runs/kallisto_collect/out/kallisto_sleuthObject.RData
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/runs/kallisto_collect/out/kallisto_tpmMatrix.csv b/runs/kallisto_collect/out/kallisto_tpmMatrix.csv
deleted file mode 100644
index b36c478..0000000
--- a/runs/kallisto_collect/out/kallisto_tpmMatrix.csv
+++ /dev/null
@@ -1,31435 +0,0 @@
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-"Tfru31404_t",0.286724835397432,0,0.493827412746989,0,0,0
-"Tfru31405_t",0,0,0,0,0,0.0274642805301062
-"Tfru31406_t",0.507104889968496,1.22112986952286,1.31008338774025,1.39877414611323,2.04827730474138,1.97875444109063
-"Tfru31407_t",14.3357156692562,2.84581764291862,21.5045981407785,212.224515842414,102.199641739142,53.4576850600056
-"Tfru31408_t",0,0,0,0,0,0
-"Tfru31409_t",18.7865724433788,18.6902313117942,19.2542141708604,9.44255153398841,11.909039069457,15.2936684292404
-"Tfru31410_t",12.8337459992563,13.1478391691407,11.6334819646125,6.72483515045318,7.89255797625976,13.2813948368555
-"Tfru31411_t",9.95867688172173,9.01846267704353,4.3979158642817,3.96195336598562,5.08333866055118,12.1435528532357
-"Tfru31412_t",0.655599519470326,0.265623826844945,0,0.68587261500485,0,0.709212228765897
-"Tfru31413_t",5.26828790504038,4.2287528342118,3.07854110499719,2.9193340591473,1.9542354576032,3.44149271144332
-"Tfru31414_t",4.4765742506988,4.91078810958502,4.62601380964053,4.78483864768352,4.26209034192634,5.78623120923271
-"Tfru31415_t",0,0.315109836527965,0,1.6242774547156,1.35913727697793,1.00526967005758
-"Tfru31416_t",3.08609547323685,1.10095518395077,4.72461818562834,1.41875663391485,0.593582402598523,2.25790015688735
-"Tfru31417_t",0,0,0,0,0,0
-"Tfru31418_t",0,0,0,0,0,0
-"Tfru31419_t",0.0182829982092377,0,0,0,0,0.0267530184227977
-"Tfru31420_t",2.42337625302252,1.78309748842988,2.60861956613343,1.46224016055527,0.873964474979796,0.886515285957371
-"Tfru31421_t",2.0834573439319,1.56445731639404,1.73629718321841,0.486633525432794,0.465368603637242,0.68840867005543
-"Tfru31422_t",5.77760288072329,5.12289722240187,7.60772622928233,4.69066130215251,7.41384658183581,5.92286262221392
-"Tfru31423_t",5.88399526025702,2.62387179054415,3.37801008408252,2.02876678195995,0.848799739124347,4.78327313823951
-"Tfru31424_t",3.33686075961357,2.99354344701567,4.39483321297496,3.2485549094312,3.90751967131154,4.16468863309569
-"Tfru31425_t",115.851568824009,122.737642964533,135.551395013929,40.193041256303,21.3314703888859,18.6895899257937
-"Tfru31426_t",5.90513426228543,5.43512786453671,6.23786866823235,14.6595987712383,15.810320414105,12.0971532929141
-"Tfru31427_t",0,0,0,0,0,0
-"Tfru31428_t",0,0,0,0,0,0
-"Tfru31429_t",0.115082707906092,0.0461873322034141,0.0991037205033341,0.0595197560460854,0,0.0420993560454642
-"Tfru31430_t",0.913156269254864,0,0,0.708414487722429,0.395183936512604,0
-"Tfru31431_t",382.216970919618,419.256022769115,412.739212689341,571.943963453987,445.607405679208,352.183127864385
-"Tfru31432_t",74.8409327628316,79.0232842657612,90.2251949593327,67.8012500484394,108.281613298853,135.168477188002
-"Tfru31433_t",22.3954100105926,24.1137401238341,21.4889051609584,21.5363464109528,16.3638531191259,20.0445353403519
-"Tfru31434_t",9.41495598052051,12.7891129702441,6.23669962787562,6.74215164978073,6.26843483041352,5.82858323651105
diff --git a/runs/kallisto_collect/run.cwl b/runs/kallisto_collect/run.cwl
new file mode 100644
index 0000000..1d3f6bb
--- /dev/null
+++ b/runs/kallisto_collect/run.cwl
@@ -0,0 +1,27 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: Workflow
+
+inputs:
+  in_kallisto_results:  Directory
+  in_metadata_file: File
+  in_metadata_sample:  string
+  in_metadata_factor:  string
+  out_folder: string
+
+steps: 
+  collectResults:
+    run: ../../workflows/kallisto_collect/workflow.cwl
+    in:
+      in_kallisto_results: in_kallisto_results
+      in_metadata_file: in_metadata_file
+      in_metadata_sample: in_metadata_sample
+      in_metadata_factor: in_metadata_factor
+      out_folder: out_folder
+    out: [outdir]
+
+outputs:
+ outdir:
+    type: Directory[]
+    outputSource: collectResults/outdir
diff --git a/runs/kallisto_collect/run.yml b/runs/kallisto_collect/run.yml
index ba0dd18..d39e600 100644
--- a/runs/kallisto_collect/run.yml
+++ b/runs/kallisto_collect/run.yml
@@ -6,4 +6,4 @@ in_metadata_file:
   path: ../merged_isa_metadata/out/merged_isa.tsv
 in_metadata_sample: "Sample.Name.2"
 in_metadata_factor: "Factor..Photosynthesis.mode."
-out_folder: out
+out_folder: results
diff --git a/workflows/deseq2/deseq2.R b/workflows/deseq2/deseq2.R
index be32d9c..0d5f022 100644
--- a/workflows/deseq2/deseq2.R
+++ b/workflows/deseq2/deseq2.R
@@ -11,8 +11,8 @@ library("readxl")
 # ## Tests 
 
 # inKallistoResults <- "../../runs/kallisto/kallisto_results"
-# inMetadataFile <- "../../runs/isaSampleToRawDataSeq-run/rnaseq-samples.xlsx"
-# inMetadataSample <- "Input [Source Name]"
+# inMetadataFile <- "../../runs/isaSampleToRawDataSeq/rnaseq-samples.xlsx"
+# inMetadataSample <- "Input [Sample Name]"
 # inMetadataFactorList <- list("Factor [Photosynthesis mode]")
 
 ### Read arguments from CLI
diff --git a/workflows/kallisto_collect/Dockerfile b/workflows/kallisto_collect/Dockerfile
new file mode 100644
index 0000000..39a6609
--- /dev/null
+++ b/workflows/kallisto_collect/Dockerfile
@@ -0,0 +1,29 @@
+# Use an official R base image
+FROM rocker/r-ver:4.1.3
+
+# Install system dependencies for R packages and other utilities
+RUN apt-get update && apt-get install -y \
+    libcurl4-openssl-dev \
+    libssl-dev \
+    libxml2-dev \
+    git \
+    build-essential \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install BiocManager
+RUN R -e "install.packages('BiocManager')"
+
+# Install Bioconductor version 3.14
+RUN R -e "BiocManager::install(version = '3.11')"
+
+# Install sleuth from Bioconductor
+RUN R -e "BiocManager::install('sleuth')"
+
+# Install other necessary CRAN packages
+RUN R -e "install.packages('jsonlite', repos='https://cran.r-project.org')"
+
+# Set the working directory to /app
+WORKDIR /app
+
+# Default command to run when the container starts
+CMD ["R"]
diff --git a/workflows/kallisto_collect/kallisto_collect.R b/workflows/kallisto_collect/kallisto_collect.R
index b2023ff..1386c9f 100644
--- a/workflows/kallisto_collect/kallisto_collect.R
+++ b/workflows/kallisto_collect/kallisto_collect.R
@@ -4,14 +4,8 @@
 #### Load required library
 ################################################
 
-if(!"BiocManager" %in% row.names(installed.packages())){install.packages('BiocManager')}
-
-if(!"sleuth" %in% row.names(installed.packages())){
-  BiocManager::install('pachterlab/sleuth')
-}
-if(!"tidyverse" %in% row.names(installed.packages())){install.packages("tidyverse")}
-if(!"openxlsx" %in% row.names(installed.packages())){install.packages("openxlsx")}
-if(!"jsonlite" %in% row.names(installed.packages())){install.packages("jsonlite")}
+library('sleuth')
+library("jsonlite")
 
 ################################################
 #### Read arguments from CLI
@@ -25,7 +19,6 @@ in_metadata_sample <- args[3]
 in_metadata_factor <- args[4]
 out_folder <- args[5]
 
-
 ################################################
 #### If it does not exist, create out dir
 ################################################
@@ -36,7 +29,7 @@ dir.create(out_folder, recursive = T, showWarnings = F)
 #### Read ISA sample metadata
 ################################################
 
-samples <- read.table(file = in_metadata_file, sep = "\t")
+samples <- read.table(file = in_metadata_file, sep = "\t", header = TRUE)
 
 ################################################
 #### Read Kallisto results
@@ -57,12 +50,10 @@ path_df <- data.frame(path = kal_dirs, out_name = gsub(".+/", "", kal_dirs))
 s2c <- merge(s2c, path_df, by = "out_name")
 
 # Build a sleuth object
-
 so <- sleuth_prep(s2c, full_model = ~condition, num_cores = 1)
 
 save(so, file = paste(out_folder, "kallisto_sleuthObject.RData", sep = "/"))
 
-
 ################################################
 #### Extract expression tables
 ################################################
@@ -74,21 +65,20 @@ expression_data <- kallisto_table(so)
 write.csv(expression_data, paste(out_folder, "/kallisto_df.csv", sep = "/"), row.names = F)
 
 ## as tpm matrix (gene x sample)
-tpm_table <- pivot_wider(expression_data, id_cols = target_id, names_from = sample, values_from = tpm)
+# Replacing pivot_wider() with base R operations
+tpm_table <- reshape(expression_data, idvar = "target_id", timevar = "sample", direction = "wide", v.names = "tpm")
 
-## write to file
+# Write to file
 write.csv(tpm_table, paste(out_folder, "/kallisto_tpmMatrix.csv", sep = "/"), row.names = F)
 
 ################################################
 #### Summarize mapping stats
 ################################################
 
-mapping_stats <- c()
-for (i in dir(kal_dirs, pattern = ".json", full.names = T))
-{
+mapping_stats <- list()
+for (i in dir(kal_dirs, pattern = ".json", full.names = T)) {
   id <- unlist(strsplit(i, split = "/"))
-
-  z <- data.frame(ID = id[length(id) - 1], read_json(i, simplifyVector = T))
+  z <- data.frame(ID = id[length(id) - 1], fromJSON(i, simplifyVector = T))
   mapping_stats <- rbind(mapping_stats, z)
 }
 
diff --git a/workflows/kallisto_collect/kallisto_collect.cwl b/workflows/kallisto_collect/kallisto_collect.cwl
deleted file mode 100644
index 6428310..0000000
--- a/workflows/kallisto_collect/kallisto_collect.cwl
+++ /dev/null
@@ -1,46 +0,0 @@
-#!/usr/bin/env cwl-runner
-
-cwlVersion: v1.2
-class: CommandLineTool
-
-requirements:
-  - class: InitialWorkDirRequirement
-    listing:
-      - entryname: kallisto_collect.R
-        entry:
-          $include: kallisto_collect.R
-  - class: NetworkAccess
-    networkAccess: true
-
-baseCommand: [Rscript, kallisto_collect.R]
-
-inputs:
-
-- id: in_kallisto_results
-  type: Directory
-  inputBinding:
-    position: 1
-- id: in_metadata_file
-  type: File
-  inputBinding:
-    position: 2
-- id: in_metadata_sample
-  type: string
-  inputBinding:
-    position: 3
-- id: in_metadata_factor
-  type: string
-  inputBinding:
-    position: 4
-- id: out_folder
-  type: string
-  inputBinding:
-    position: 5
-
-outputs:
-- id: outdir
-  type:
-    type: array
-    items: Directory
-  outputBinding:
-    glob: $(runtime.outdir)/$(inputs.out_folder)
diff --git a/workflows/kallisto_collect/workflow.cwl b/workflows/kallisto_collect/workflow.cwl
new file mode 100644
index 0000000..28a198f
--- /dev/null
+++ b/workflows/kallisto_collect/workflow.cwl
@@ -0,0 +1,52 @@
+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: CommandLineTool
+
+hints:
+  # DockerRequirement:
+  #   dockerImageId: "sleuth"
+  #   dockerFile: {$include: "Dockerfile"}
+  DockerRequirement: 
+    dockerPull: quay.io/biocontainers/mulled-v2-fdd016122f200fdc6dc30f6ea2fd0000e8067dff:f9531f6ac1f44332eff70b5912d7d5f3ebe8df38-0
+
+requirements:
+  - class: InitialWorkDirRequirement
+    listing:
+      - entryname: kallisto_collect.R
+        entry:
+          $include: kallisto_collect.R
+  - class: NetworkAccess
+    networkAccess: true
+
+baseCommand: [Rscript, kallisto_collect.R]
+
+inputs:
+  - id: in_kallisto_results
+    type: Directory
+    inputBinding:
+      position: 1
+  - id: in_metadata_file
+    type: File
+    inputBinding:
+      position: 2
+  - id: in_metadata_sample
+    type: string
+    inputBinding:
+      position: 3
+  - id: in_metadata_factor
+    type: string
+    inputBinding:
+      position: 4
+  - id: out_folder
+    type: string
+    inputBinding:
+      position: 5
+
+outputs:
+- id: outdir
+  type:
+    type: array
+    items: Directory
+  outputBinding:
+    glob: $(runtime.outdir)/$(inputs.out_folder)
-- 
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