Merge pull request #124 from daichengxin/dev

fixed error

assets/PXD026600.sdrf.tsv

@@ -1,4 +1,3 @@
 Source Name	Characteristics[organism]	Characteristics[organism part]	Characteristics[age]	Characteristics[strain]	Characteristics[developmental stage]	Characteristics[cell line]	Characteristics[cell type]	Characteristics[sex]	Characteristics[disease]	characteristics[mass]	characteristics[spiked compound]	Characteristics[biological replicate]	Material Type	assay name	technology type	comment[data file]	comment[file uri]	comment[technical replicate]	comment[fraction identifier]	comment[proteomics data acquisition method]	comment[label]	comment[instrument]	comment[modification parameters]	comment[modification parameters]	comment[cleavage agent details]	comment[dissociation method]	comment[collision energy]	comment[precursor mass tolerance]	comment[fragment mass tolerance]	factor value[spiked compound]
 Sample 1	Escherichia coli K-12	whole plant	not available	K12	not available	not applicable	not available	not available	not available	1 ug	CT=Mixture;CN=UPS1;QY=0.1 fmol	1	whole organism	run 1	proteomic profiling by mass spectrometry	RD139_Narrow_UPS1_0_1fmol_inj1.raw	ftp://massive.ucsd.edu/MSV000087597/raw/RD139_Raw_files_DIA_Narrow/RD139_Narrow_UPS1_0_1fmol_inj1.raw	1	1	NT=Data-Independent Acquisition;AC=NCIT:C161786	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion;AC=MS:1002416	NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35	NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4	AC=MS:1001313;NT=Trypsin	NT=HCD;AC=PRIDE:0000590	35% CE	10 ppm	20 mmu	CT=Mixture;CN=UPS1;QY=0.1 fmol
 Sample 1	Escherichia coli K-12	whole plant	not available	K12	not available	not applicable	not available	not available	not available	1 ug	CT=Mixture;CN=UPS1;QY=0.1 fmol	1	whole organism	run 2	proteomic profiling by mass spectrometry	RD139_Narrow_UPS1_0_1fmol_inj2.raw	ftp://massive.ucsd.edu/MSV000087597/raw/RD139_Raw_files_DIA_Narrow/RD139_Narrow_UPS1_0_1fmol_inj2.raw	2	1	NT=Data-Independent Acquisition;AC=NCIT:C161786	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion;AC=MS:1002416	NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35	NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4	AC=MS:1001313;NT=Trypsin	NT=HCD;AC=PRIDE:0000590	35% CE	10 ppm	20 mmu	CT=Mixture;CN=UPS1;QY=0.1 fmol
-Sample 1	Escherichia coli K-12	whole plant	not available	K12	not available	not applicable	not available	not available	not available	1 ug	CT=Mixture;CN=UPS1;QY=0.1 fmol	1	whole organism	run 3	proteomic profiling by mass spectrometry	RD139_Narrow_UPS1_0_1fmol_inj3.raw	ftp://massive.ucsd.edu/MSV000087597/raw/RD139_Raw_files_DIA_Narrow/RD139_Narrow_UPS1_0_1fmol_inj3.raw	3	1	NT=Data-Independent Acquisition;AC=NCIT:C161786	AC=MS:1002038;NT=label free sample	NT=Orbitrap Fusion;AC=MS:1002416	NT=Oxidation;MT=Variable;TA=M;AC=Unimod:35	NT=Carbamidomethyl;TA=C;MT=fixed;AC=UNIMOD:4	AC=MS:1001313;NT=Trypsin	NT=HCD;AC=PRIDE:0000590	35% CE	10 ppm	20 mmu	CT=Mixture;CN=UPS1;QY=0.1 fmol

bin/prepare_diann_parameters.py

@@ -44,31 +44,33 @@ def convert_mod(unimod_csv, fix_mod, var_mod):
     var_ptm = []
     fix_ptm = []
     unimod = pd.read_csv(unimod_csv, header=0, sep=",")
-    for mod in fix_mod.split(","):
-        diann_mod = unimod[unimod['name'] == mod.split(" ")[0]]["params"].values[0]
-        site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
-        if site == "Protein N-term":
-            site = "*n"
-        elif site == "N-term":
-            site = "n"
-
-        if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
-            fix_ptm.append(diann_mod + "," + site + "," + "label")
-        else:
-            fix_ptm.append(diann_mod + "," + site)
-
-    for mod in var_mod.split(","):
-        diann_mod = unimod[unimod['name'] == mod.split(" ")[0]]["params"].values[0]
-        site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
-        if site == "Protein N-term":
-            site = "*n"
-        elif site == "N-term":
-            site = "n"
-
-        if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
-            var_ptm.append(diann_mod + "," + site + "," + "label")
-        else:
-            var_ptm.append(diann_mod + "," + site)
+    if fix_mod != "":
+        for mod in fix_mod.split(","):
+            diann_mod = unimod[unimod['name'] == mod.split(" ")[0]]["params"].values[0]
+            site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
+            if site == "Protein N-term":
+                site = "*n"
+            elif site == "N-term":
+                site = "n"
+
+            if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
+                fix_ptm.append(diann_mod + "," + site + "," + "label")
+            else:
+                fix_ptm.append(diann_mod + "," + site)
+
+    if var_mod != "":
+        for mod in var_mod.split(","):
+            diann_mod = unimod[unimod['name'] == mod.split(" ")[0]]["params"].values[0]
+            site = re.findall(pattern, " ".join(mod.split(" ")[1:]))[0]
+            if site == "Protein N-term":
+                site = "*n"
+            elif site == "N-term":
+                site = "n"
+
+            if "TMT" in diann_mod or "Label" in diann_mod or "iTRAQ" in diann_mod or "mTRAQ" in diann_mod:
+                var_ptm.append(diann_mod + "," + site + "," + "label")
+            else:
+                var_ptm.append(diann_mod + "," + site)
 
     return fix_ptm, var_ptm
 

modules/local/thermorawfileparser/main.nf

@@ -8,6 +8,8 @@ process THERMORAWFILEPARSER {
         'https://depot.galaxyproject.org/singularity/thermorawfileparser:1.3.4--ha8f3691_0' :
         'quay.io/biocontainers/thermorawfileparser:1.3.4--ha8f3691_0' }"
 
+    stageInMode {task.attempt == 1 ? 'link' : (task.attempt == 2 ? 'symlink' : 'copy')}
+
     input:
     tuple val(meta), path(rawfile)