Skip to content

Commit b6ca511

Browse files
biodavidjmbiodavidjm
authored
Merge pull request #84 from MoTrPAC/feat/add-helper-script
Script fixes, remove redundant isPTM input parameter
2 parents 88de5a5 + fbb9be5 commit b6ca511

20 files changed

+241
-131
lines changed

‎inputs/templates/msgfplus/config-msgfplus-ac-lf.json

+7-8
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,12 @@
11
{
22
"proteomics_msgfplus.ascore_disk": 20,
3-
"proteomics_msgfplus.ascore_docker": "docker-repository/prot-ascore:v1.0.8315",
3+
"proteomics_msgfplus.ascore_docker": "docker-repository/ascore:v1.0.8315",
44
"proteomics_msgfplus.ascore_ncpu": 4,
55
"proteomics_msgfplus.ascore_parameter_p": "gcp-parameters/AScore_CID_0.5Da_ETD_0.5Da_HCD_0.05Da.xml",
66
"proteomics_msgfplus.ascore_ramGB": 15,
77
"proteomics_msgfplus.fasta_sequence_db": "gcp-sequencedb/motrpac-rat-refseq-ID_007275_FB1B42E8.fasta",
8-
"proteomics_msgfplus.isPTM": true,
98
"proteomics_msgfplus.masic_disk": 20,
10-
"proteomics_msgfplus.masic_docker": "docker-repository/prot-masic:v3.2.8286",
9+
"proteomics_msgfplus.masic_docker": "docker-repository/masic:v3.2.8286",
1110
"proteomics_msgfplus.masic_ncpu": 4,
1211
"proteomics_msgfplus.masic_parameter": "gcp-parameters/TMT11_LTQ-FT_10ppm_ReporterTol0.003Da_2017-03-17.xml",
1312
"proteomics_msgfplus.masic_ramGB": 15,
@@ -16,22 +15,22 @@
1615
"proteomics_msgfplus.msconvert_ncpu": 4,
1716
"proteomics_msgfplus.msconvert_ramGB": 15,
1817
"proteomics_msgfplus.msgf_disk": 20,
19-
"proteomics_msgfplus.msgf_docker": "docker-repository/prot-msgfplus:v2024.03.26",
18+
"proteomics_msgfplus.msgf_docker": "docker-repository/msgfplus:v2024.03.26",
2019
"proteomics_msgfplus.msgf_identification_parameter": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_6Plex_20ppmParTol_PlusOne_IsotopeError.txt",
2120
"proteomics_msgfplus.msgf_ncpu": 4,
2221
"proteomics_msgfplus.msgf_ramGB": 15,
2322
"proteomics_msgfplus.msgf_tryptic_mzrefinery_parameter": "gcp-parameters/MzRef_StatCysAlk_TMT_6plex.txt",
24-
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/prot-mzid2tsv:v1.5.1",
23+
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/mzid2tsv:v1.5.1",
2524
"proteomics_msgfplus.phrp_disk": 20,
26-
"proteomics_msgfplus.phrp_docker": "docker-repository/prot-phrp:v3.1.8904",
25+
"proteomics_msgfplus.phrp_docker": "docker-repository/phrp:v3.1.8904",
2726
"proteomics_msgfplus.phrp_ncpu": 4,
2827
"proteomics_msgfplus.phrp_parameter_m": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_6Plex_20ppmParTol_PlusOne_IsotopeError_ModDefs.txt",
2928
"proteomics_msgfplus.phrp_parameter_n": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_6Plex_20ppmParTol_PlusOne_IsotopeError.txt",
3029
"proteomics_msgfplus.phrp_parameter_t": "gcp-parameters/Mass_Correction_Tags.txt",
3130
"proteomics_msgfplus.phrp_ramGB": 15,
3231
"proteomics_msgfplus.phrp_synprob": 0.05,
3332
"proteomics_msgfplus.phrp_synpvalue": 0.02,
34-
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/prot-ppmerror:v1.2.7632",
33+
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/ppmerror:v1.2.7632",
3534
"proteomics_msgfplus.pr_ratio": "File",
3635
"proteomics_msgfplus.ptm_type": "ac",
3736
"proteomics_msgfplus.quant_method": "label-free|tmt",
@@ -42,7 +41,7 @@
4241
"proteomics_msgfplus.sd_references": "gcp-study-design/references.txt",
4342
"proteomics_msgfplus.sd_samples": "gcp-study-design/samples.txt",
4443
"proteomics_msgfplus.wrapper_disk": 80,
45-
"proteomics_msgfplus.wrapper_docker": "docker-repository/prot-plexedpiper:v0.4.1",
44+
"proteomics_msgfplus.wrapper_docker": "docker-repository/plexedpiper:v0.4.1",
4645
"proteomics_msgfplus.wrapper_ncpu": 8,
4746
"proteomics_msgfplus.wrapper_ramGB": 60
4847
}

‎inputs/templates/msgfplus/config-msgfplus-ac-tmt11.json

+7-8
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,12 @@
11
{
22
"proteomics_msgfplus.ascore_disk": 20,
3-
"proteomics_msgfplus.ascore_docker": "docker-repository/prot-ascore:v1.0.8315",
3+
"proteomics_msgfplus.ascore_docker": "docker-repository/ascore:v1.0.8315",
44
"proteomics_msgfplus.ascore_ncpu": 4,
55
"proteomics_msgfplus.ascore_parameter_p": "gcp-parameters/AScore_CID_0.5Da_ETD_0.5Da_HCD_0.05Da.xml",
66
"proteomics_msgfplus.ascore_ramGB": 15,
77
"proteomics_msgfplus.fasta_sequence_db": "gcp-sequencedb/motrpac-rat-refseq-ID_007275_FB1B42E8.fasta",
8-
"proteomics_msgfplus.isPTM": true,
98
"proteomics_msgfplus.masic_disk": 20,
10-
"proteomics_msgfplus.masic_docker": "docker-repository/prot-masic:v3.2.8286",
9+
"proteomics_msgfplus.masic_docker": "docker-repository/masic:v3.2.8286",
1110
"proteomics_msgfplus.masic_ncpu": 4,
1211
"proteomics_msgfplus.masic_parameter": "gcp-parameters/TMT11_LTQ-FT_10ppm_ReporterTol0.003Da_2017-03-17.xml",
1312
"proteomics_msgfplus.masic_ramGB": 15,
@@ -16,22 +15,22 @@
1615
"proteomics_msgfplus.msconvert_ncpu": 4,
1716
"proteomics_msgfplus.msconvert_ramGB": 15,
1817
"proteomics_msgfplus.msgf_disk": 20,
19-
"proteomics_msgfplus.msgf_docker": "docker-repository/prot-msgfplus:v2024.03.26",
18+
"proteomics_msgfplus.msgf_docker": "docker-repository/msgfplus:v2024.03.26",
2019
"proteomics_msgfplus.msgf_identification_parameter": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_6Plex_20ppmParTol_PlusOne_IsotopeError.txt",
2120
"proteomics_msgfplus.msgf_ncpu": 4,
2221
"proteomics_msgfplus.msgf_ramGB": 15,
2322
"proteomics_msgfplus.msgf_tryptic_mzrefinery_parameter": "gcp-parameters/MzRef_StatCysAlk_TMT_6plex.txt",
24-
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/prot-mzid2tsv:v1.5.1",
23+
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/mzid2tsv:v1.5.1",
2524
"proteomics_msgfplus.phrp_disk": 20,
26-
"proteomics_msgfplus.phrp_docker": "docker-repository/prot-phrp:v3.1.8904",
25+
"proteomics_msgfplus.phrp_docker": "docker-repository/phrp:v3.1.8904",
2726
"proteomics_msgfplus.phrp_ncpu": 4,
2827
"proteomics_msgfplus.phrp_parameter_m": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_6Plex_20ppmParTol_PlusOne_IsotopeError_ModDefs.txt",
2928
"proteomics_msgfplus.phrp_parameter_n": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_6Plex_20ppmParTol_PlusOne_IsotopeError.txt",
3029
"proteomics_msgfplus.phrp_parameter_t": "gcp-parameters/Mass_Correction_Tags.txt",
3130
"proteomics_msgfplus.phrp_ramGB": 15,
3231
"proteomics_msgfplus.phrp_synprob": 0.05,
3332
"proteomics_msgfplus.phrp_synpvalue": 0.02,
34-
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/prot-ppmerror:v1.2.7632",
33+
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/ppmerror:v1.2.7632",
3534
"proteomics_msgfplus.pr_ratio": "File",
3635
"proteomics_msgfplus.quant_method": "tmt",
3736
"proteomics_msgfplus.raw_file": ["gcp-raw/file1.raw", "gcp-raw/file2.raw"],
@@ -41,7 +40,7 @@
4140
"proteomics_msgfplus.sd_references": "gcp-study-design/references.txt",
4241
"proteomics_msgfplus.sd_samples": "gcp-study-design/samples.txt",
4342
"proteomics_msgfplus.wrapper_disk": 80,
44-
"proteomics_msgfplus.wrapper_docker": "docker-repository/prot-plexedpiper:v0.4.1",
43+
"proteomics_msgfplus.wrapper_docker": "docker-repository/plexedpiper:v0.4.1",
4544
"proteomics_msgfplus.wrapper_ncpu": 8,
4645
"proteomics_msgfplus.wrapper_ramGB": 60,
4746
"proteomics_msgfplus.proteomics_experiment": "String",

‎inputs/templates/msgfplus/config-msgfplus-ac-tmt16.json

+7-8
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,12 @@
11
{
22
"proteomics_msgfplus.ascore_disk": 20,
3-
"proteomics_msgfplus.ascore_docker": "docker-repository/prot-ascore:v1.0.8315",
3+
"proteomics_msgfplus.ascore_docker": "docker-repository/ascore:v1.0.8315",
44
"proteomics_msgfplus.ascore_ncpu": 4,
55
"proteomics_msgfplus.ascore_parameter_p": "gcp-parameters/AScore_CID_0.5Da_ETD_0.5Da_HCD_0.05Da.xml",
66
"proteomics_msgfplus.ascore_ramGB": 15,
77
"proteomics_msgfplus.fasta_sequence_db": "gcp-sequencedb/motrpac-rat-refseq-ID_007275_FB1B42E8.fasta",
8-
"proteomics_msgfplus.isPTM": true,
98
"proteomics_msgfplus.masic_disk": 20,
10-
"proteomics_msgfplus.masic_docker": "docker-repository/prot-masic:v3.2.8286",
9+
"proteomics_msgfplus.masic_docker": "docker-repository/masic:v3.2.8286",
1110
"proteomics_msgfplus.masic_ncpu": 4,
1211
"proteomics_msgfplus.masic_parameter": "gcp-parameters/TMT16_10ppm_ReporterTol0.003Da_2019-10-07.xml",
1312
"proteomics_msgfplus.masic_ramGB": 15,
@@ -16,22 +15,22 @@
1615
"proteomics_msgfplus.msconvert_ncpu": 4,
1716
"proteomics_msgfplus.msconvert_ramGB": 15,
1817
"proteomics_msgfplus.msgf_disk": 20,
19-
"proteomics_msgfplus.msgf_docker": "docker-repository/prot-msgfplus:v2024.03.26",
18+
"proteomics_msgfplus.msgf_docker": "docker-repository/msgfplus:v2024.03.26",
2019
"proteomics_msgfplus.msgf_identification_parameter": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_16Plex_20ppmParTol_PlusOne_IsotopeError.txt",
2120
"proteomics_msgfplus.msgf_ncpu": 4,
2221
"proteomics_msgfplus.msgf_ramGB": 15,
2322
"proteomics_msgfplus.msgf_tryptic_mzrefinery_parameter": "gcp-parameters/MzRef_StatCysAlk_TMT_16plex.txt",
24-
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/prot-mzid2tsv:v1.5.1",
23+
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/mzid2tsv:v1.5.1",
2524
"proteomics_msgfplus.phrp_disk": 20,
26-
"proteomics_msgfplus.phrp_docker": "docker-repository/prot-phrp:v3.1.8904",
25+
"proteomics_msgfplus.phrp_docker": "docker-repository/phrp:v3.1.8904",
2726
"proteomics_msgfplus.phrp_ncpu": 4,
2827
"proteomics_msgfplus.phrp_parameter_m": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_16Plex_20ppmParTol_PlusOne_IsotopeError_ModDefs.txt",
2928
"proteomics_msgfplus.phrp_parameter_n": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_16Plex_20ppmParTol_PlusOne_IsotopeError.txt",
3029
"proteomics_msgfplus.phrp_parameter_t": "gcp-parameters/Mass_Correction_Tags.txt",
3130
"proteomics_msgfplus.phrp_ramGB": 15,
3231
"proteomics_msgfplus.phrp_synprob": 0.05,
3332
"proteomics_msgfplus.phrp_synpvalue": 0.02,
34-
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/prot-ppmerror:v1.2.7632",
33+
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/ppmerror:v1.2.7632",
3534
"proteomics_msgfplus.pr_ratio": "File",
3635
"proteomics_msgfplus.quant_method": "tmt",
3736
"proteomics_msgfplus.raw_file": ["gcp-raw/file1.raw", "gcp-raw/file2.raw"],
@@ -41,7 +40,7 @@
4140
"proteomics_msgfplus.sd_references": "gcp-study-design/references.txt",
4241
"proteomics_msgfplus.sd_samples": "gcp-study-design/samples.txt",
4342
"proteomics_msgfplus.wrapper_disk": 80,
44-
"proteomics_msgfplus.wrapper_docker": "docker-repository/prot-plexedpiper:v0.4.1",
43+
"proteomics_msgfplus.wrapper_docker": "docker-repository/plexedpiper:v0.4.1",
4544
"proteomics_msgfplus.wrapper_ncpu": 8,
4645
"proteomics_msgfplus.wrapper_ramGB": 60,
4746
"proteomics_msgfplus.proteomics_experiment": "String",

‎inputs/templates/msgfplus/config-msgfplus-ac-tmt18.json

+7-8
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,12 @@
11
{
22
"proteomics_msgfplus.ascore_disk": 20,
3-
"proteomics_msgfplus.ascore_docker": "docker-repository/prot-ascore:v1.0.8315",
3+
"proteomics_msgfplus.ascore_docker": "docker-repository/ascore:v1.0.8315",
44
"proteomics_msgfplus.ascore_ncpu": 4,
55
"proteomics_msgfplus.ascore_parameter_p": "gcp-parameters/AScore_CID_0.5Da_ETD_0.5Da_HCD_0.05Da.xml",
66
"proteomics_msgfplus.ascore_ramGB": 15,
77
"proteomics_msgfplus.fasta_sequence_db": "gcp-sequencedb/motrpac-rat-refseq-ID_007275_FB1B42E8.fasta",
8-
"proteomics_msgfplus.isPTM": true,
98
"proteomics_msgfplus.masic_disk": 20,
10-
"proteomics_msgfplus.masic_docker": "docker-repository/prot-masic:v3.2.8286",
9+
"proteomics_msgfplus.masic_docker": "docker-repository/masic:v3.2.8286",
1110
"proteomics_msgfplus.masic_ncpu": 4,
1211
"proteomics_msgfplus.masic_parameter": "gcp-parameters/TMT18_10ppm_ReporterTol0.003Da_2021-01-24.xml",
1312
"proteomics_msgfplus.masic_ramGB": 15,
@@ -16,22 +15,22 @@
1615
"proteomics_msgfplus.msconvert_ncpu": 4,
1716
"proteomics_msgfplus.msconvert_ramGB": 15,
1817
"proteomics_msgfplus.msgf_disk": 20,
19-
"proteomics_msgfplus.msgf_docker": "docker-repository/prot-msgfplus:v2024.03.26",
18+
"proteomics_msgfplus.msgf_docker": "docker-repository/msgfplus:v2024.03.26",
2019
"proteomics_msgfplus.msgf_identification_parameter": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_16Plex_20ppmParTol_PlusOne_IsotopeError.txt",
2120
"proteomics_msgfplus.msgf_ncpu": 4,
2221
"proteomics_msgfplus.msgf_ramGB": 15,
2322
"proteomics_msgfplus.msgf_tryptic_mzrefinery_parameter": "gcp-parameters/MzRef_StatCysAlk_TMT_16plex.txt",
24-
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/prot-mzid2tsv:v1.5.1",
23+
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/mzid2tsv:v1.5.1",
2524
"proteomics_msgfplus.phrp_disk": 20,
26-
"proteomics_msgfplus.phrp_docker": "docker-repository/prot-phrp:v3.1.8904",
25+
"proteomics_msgfplus.phrp_docker": "docker-repository/phrp:v3.1.8904",
2726
"proteomics_msgfplus.phrp_ncpu": 4,
2827
"proteomics_msgfplus.phrp_parameter_m": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_16Plex_20ppmParTol_PlusOne_IsotopeError_ModDefs.txt",
2928
"proteomics_msgfplus.phrp_parameter_n": "gcp-parameters/MSGFPlus_Tryp_DynMetOx_TMTExclusive_K_Acetyl_K_Carbamyl_N_Deamid_Stat_CysAlk_TMT_16Plex_20ppmParTol_PlusOne_IsotopeError.txt",
3029
"proteomics_msgfplus.phrp_parameter_t": "gcp-parameters/Mass_Correction_Tags.txt",
3130
"proteomics_msgfplus.phrp_ramGB": 15,
3231
"proteomics_msgfplus.phrp_synprob": 0.05,
3332
"proteomics_msgfplus.phrp_synpvalue": 0.02,
34-
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/prot-ppmerror:v1.2.7632",
33+
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/ppmerror:v1.2.7632",
3534
"proteomics_msgfplus.pr_ratio": "File",
3635
"proteomics_msgfplus.quant_method": "tmt",
3736
"proteomics_msgfplus.raw_file": ["gcp-raw/file1.raw", "gcp-raw/file2.raw"],
@@ -41,7 +40,7 @@
4140
"proteomics_msgfplus.sd_references": "gcp-study-design/references.txt",
4241
"proteomics_msgfplus.sd_samples": "gcp-study-design/samples.txt",
4342
"proteomics_msgfplus.wrapper_disk": 80,
44-
"proteomics_msgfplus.wrapper_docker": "docker-repository/prot-plexedpiper:v0.4.1",
43+
"proteomics_msgfplus.wrapper_docker": "docker-repository/plexedpiper:v0.4.1",
4544
"proteomics_msgfplus.wrapper_ncpu": 8,
4645
"proteomics_msgfplus.wrapper_ramGB": 60,
4746
"proteomics_msgfplus.proteomics_experiment": "String",

‎inputs/templates/msgfplus/config-msgfplus-ph-lf.json

+7-8
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,12 @@
11
{
22
"proteomics_msgfplus.ascore_disk": 20,
3-
"proteomics_msgfplus.ascore_docker": "docker-repository/prot-ascore:v1.0.8315",
3+
"proteomics_msgfplus.ascore_docker": "docker-repository/ascore:v1.0.8315",
44
"proteomics_msgfplus.ascore_ncpu": 4,
55
"proteomics_msgfplus.ascore_parameter_p": "gcp-parameters/AScore_CID_0.5Da_ETD_0.5Da_HCD_0.05Da.xml",
66
"proteomics_msgfplus.ascore_ramGB": 15,
77
"proteomics_msgfplus.fasta_sequence_db": "gcp-sequencedb/motrpac-rat-refseq-ID_007275_FB1B42E8.fasta",
8-
"proteomics_msgfplus.isPTM": true,
98
"proteomics_msgfplus.masic_disk": 20,
10-
"proteomics_msgfplus.masic_docker": "docker-repository/prot-masic:v3.2.8286",
9+
"proteomics_msgfplus.masic_docker": "docker-repository/masic:v3.2.8286",
1110
"proteomics_msgfplus.masic_ncpu": 4,
1211
"proteomics_msgfplus.masic_parameter": "gcp-parameters/LTQ-FT_10ppm_2014-08-06.xml",
1312
"proteomics_msgfplus.masic_ramGB": 15,
@@ -16,22 +15,22 @@
1615
"proteomics_msgfplus.msconvert_ncpu": 4,
1716
"proteomics_msgfplus.msconvert_ramGB": 15,
1817
"proteomics_msgfplus.msgf_disk": 20,
19-
"proteomics_msgfplus.msgf_docker": "docker-repository/prot-msgfplus:v2024.03.26",
18+
"proteomics_msgfplus.msgf_docker": "docker-repository/msgfplus:v2024.03.26",
2019
"proteomics_msgfplus.msgf_identification_parameter": "gcp-parameters/MSGFPlus_Tryp_DynSTYPhos_Stat_CysAlk_20ppmParTol.txt",
2120
"proteomics_msgfplus.msgf_ncpu": 4,
2221
"proteomics_msgfplus.msgf_ramGB": 15,
2322
"proteomics_msgfplus.msgf_tryptic_mzrefinery_parameter": "gcp-parameters/MzRef_StatCysAlk.txt",
24-
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/prot-mzid2tsv:v1.5.1",
23+
"proteomics_msgfplus.mzidtotsvconverter_docker": "docker-repository/mzid2tsv:v1.5.1",
2524
"proteomics_msgfplus.phrp_disk": 20,
26-
"proteomics_msgfplus.phrp_docker": "docker-repository/prot-phrp:v3.1.8904",
25+
"proteomics_msgfplus.phrp_docker": "docker-repository/phrp:v3.1.8904",
2726
"proteomics_msgfplus.phrp_ncpu": 4,
2827
"proteomics_msgfplus.phrp_parameter_m": "gcp-parameters/MSGFPlus_Tryp_DynSTYPhos_Stat_CysAlk_20ppmParTol_ModDefs.txt",
2928
"proteomics_msgfplus.phrp_parameter_n": "gcp-parameters/MSGFPlus_Tryp_DynSTYPhos_Stat_CysAlk_20ppmParTol.txt",
3029
"proteomics_msgfplus.phrp_parameter_t": "gcp-parameters/Mass_Correction_Tags.txt",
3130
"proteomics_msgfplus.phrp_ramGB": 15,
3231
"proteomics_msgfplus.phrp_synprob": 0.05,
3332
"proteomics_msgfplus.phrp_synpvalue": 0.02,
34-
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/prot-ppmerror:v1.2.7632",
33+
"proteomics_msgfplus.ppm_errorcharter_docker": "docker-repository/ppmerror:v1.2.7632",
3534
"proteomics_msgfplus.pr_ratio": "File",
3635
"proteomics_msgfplus.ptm_type": "ph",
3736
"proteomics_msgfplus.quant_method": "label-free",
@@ -42,7 +41,7 @@
4241
"proteomics_msgfplus.sd_references": "gcp-study-design/references.txt",
4342
"proteomics_msgfplus.sd_samples": "gcp-study-design/samples.txt",
4443
"proteomics_msgfplus.wrapper_disk": 80,
45-
"proteomics_msgfplus.wrapper_docker": "docker-repository/prot-plexedpiper:v0.4.1",
44+
"proteomics_msgfplus.wrapper_docker": "docker-repository/plexedpiper:v0.4.1",
4645
"proteomics_msgfplus.wrapper_ncpu": 8,
4746
"proteomics_msgfplus.wrapper_ramGB": 60
4847
}

0 commit comments

Comments
 (0)