new: added nextflow workflow

.gitignore

@@ -4,3 +4,4 @@ logs/
 .DS_Store
 *.pyc
 .vscode
+.nextflow*

main.nf

@@ -1,5 +1,15 @@
-include { Hello } from './modules/hello'
+include { MAKE_TRANSFORMATION_PROTOCOL; MAKE_SPOTTING_PROTOCOL } from './modules/protocol_compiler'
 
 workflow {
-    channel.fromPath("${params.inputFile}") | Hello
+
+    MAKE_TRANSFORMATION_PROTOCOL(
+        tuple(file("$params.transformation_config"), file("$params.transformation_data")), 
+        file("$params.protocol_template_dir")
+    )
+
+    MAKE_SPOTTING_PROTOCOL(
+        tuple(file("$params.spotting_config"), file("$params.spotting_data")), 
+        file("$params.protocol_template_dir")
+    )
+
 }

modules/protocol_compiler/main.nf

@@ -1,31 +1,47 @@
 process MAKE_TRANSFORMATION_PROTOCOL {
 
-    publishDir "${params.resultsDir}", pattern: "results.txt", mode: 'copy'
+    publishDir "${params.resultsDir}", pattern: "transformation_protocol.py", mode: 'copy'
 
     input:
-        path data
+        tuple path(config), path(csv)
+        path(template_dir)
 
     output:
-        path 'results.txt'
+        path 'transformation_protocol.py'
 
+    script:
     """
-        cat ${data} > results.txt
+        protocol-compiler.py -d ${template_dir} -o transformation_protocol.py \
+            transformation-template.py ${config} ${csv}
+    """
+
+    stub: 
+    """
+        touch transformation_protocol.py
     """
 
 }
 
 process MAKE_SPOTTING_PROTOCOL {
 
-    publishDir "${params.resultsDir}", pattern: "results.txt", mode: 'copy'
+    publishDir "${params.resultsDir}", pattern: "spotting_protocol.py", mode: 'copy'
 
     input:
-        path data
+        tuple path(config), path(csv)
+        path(template_dir)
 
     output:
-        path 'results.txt'
+        path 'spotting_protocol.py'
+
+    script:
+    """
+        protocol-compiler.py -d ${template_dir} -o spotting_protocol.py \
+            spotting-template.py ${config} ${csv}
+    """
 
+    stub: 
     """
-        cat ${data} > results.txt
+        touch spotting_protocol.py
     """
 
 }

modules/protocol_compiler/requirements.txt

@@ -0,0 +1,3 @@
+opentrons
+jinja2
+docopt

nextflow.config

@@ -6,13 +6,25 @@
 includeConfig 'conf/base.config' 
 includeConfig 'conf/modules.config' 
 
-
 /* 
 ====================================================================
 |                 WORKFLOW INPUT PARAMETERS
 ====================================================================
 */
 params {
-  inputFile = "./testdata/mydata.txt"
+  /* */
+  protocol_template_dir = "${baseDir}/assets/protocols"
+
+  /* */
+  transformation_config = "${baseDir}/assets/testdata/transformation-parameters.json"
+  transformation_data = "${baseDir}/assets/testdata/transformation-data.csv"
+
+  /* */
+  spotting_config = "${baseDir}/assets/testdata/spotting-parameters.json"
+  spotting_data = "${baseDir}/assets/testdata/spotting-data.csv"
+
+  /* */
   resultsDir = "./results/"
 }
+
+process.container = 'ghcr.io/stracquadaniolab/opentrons:latest'

readme.md

@@ -8,52 +8,52 @@ End-to-end eznyme screening platform for argB.
 ## Configuration
 
 **Experiment parameters**
-- transformations_n: number of transformations to be spotted (default: 24)
-- dna_volume: volume of DNA in µL (default: 2)
-- cc_volume: volume of competent cells in µL (default: 20)
-- soc_volume: volume of SOC media in µL (default: 178)
-- competent_cells_well: name of the well containing competent cells (defualt: "H12")
-- init_temp: thermocycler inital temperature before heat-shock transformation (default: 4)
-- init_time: thermocycler inital time before heat-shock transformation (default: 20)
-- heat_temp: thermocycler heat temperature during heat-shock transformation (default: 42)
-- heat_time: thermocycler heat temperature during heat-shock transformation (default: 1)
-- cool_temp: thermocycler cooling temperature after heat-shock transformation (default: 4)
-- cool_time: thermocycler cooling temperature after heat-shock transformation (default: 2)
-- inc_temp: thermocycler incubation temperature after heat-shock transformation (default: 37)
-- inc_time: thermocycler incubation temperature agter heat-shock transformation (default: 60)
-- spot_volume: spot volume for agar plate in µL (default: 5)
+- `transformations_n`: number of transformations to be spotted (default: 24)
+- `dna_volume`: volume of DNA in µL (default: 2)
+- `cc_volume`: volume of competent cells in µL (default: 20)
+- `soc_volume`: volume of SOC media in µL (default: 178)
+- `competent_cells_well`: name of the well containing competent cells (defualt: "H12")
+- `init_temp`: thermocycler inital temperature before heat-shock transformation (default: 4)
+- `init_time`: thermocycler inital time before heat-shock transformation (default: 20)
+- `heat_temp`: thermocycler heat temperature during heat-shock transformation (default: 42)
+- `heat_time`: thermocycler heat temperature during heat-shock transformation (default: 1)
+- `cool_temp`: thermocycler cooling temperature after heat-shock transformation (default: 4)
+- `cool_time`: thermocycler cooling temperature after heat-shock transformation (default: 2)
+- `inc_temp`: thermocycler incubation temperature after heat-shock transformation (default: 37)
+- `inc_time`: thermocycler incubation temperature agter heat-shock transformation (default: 60)
+- `spot_volume`: spot volume for agar plate in µL (default: 5)
 
 **Hardware and labware names and location**
-- dna_plate_loadname: name of the plate containing DNA to be transformed (default: "armadillo_96_wellplate_200ul_pcr_full_skirt")
-- dna_plate_slot: 2
-- reservoir_loadname: name of the reservoir containing SOC media and competent cells
-- reservoir_slot: 3
-- transformation_plate_loadname: name of the plate where transformation occurs (default: "armadillo_96_wellplate_200ul_pcr_full_skirt")
-- agar_plate_loadname: name of the agar plate (default: "nunc_singlewell_plate_90ml_4x6_grid")
-- agar_def_json: name of the json file with the custom agar plate definition (default: "nunc_singlewell_plate_90ml_4x6_grid")
-- agar_max_wells_n: maximum number of wells on the agar plate (default: 24)
-- agar_slot: location of the agar plates given as a list (default: [1])
-- p20_tiprack_loadname: name of the p20 tiprack (default: "opentrons_96_tiprack_20ul")
-- p20_tiprack_slot: location of the p20 tiprack (Default: 6)
-- p20_name: name of the p20 pipette (default: "p20_single_gen2")
-- p20_mount: location of the p20 pipette mount (default: "right")
-- p300_tiprack_loadname: name of the p300 tiprack (default: "opentrons_96_tiprack_300ul")
-- p300_tiprack_slot: location of the p300 tiprack (Default: 9)
-- p300_name: name of the p300 pipette (default: "p300_multi_gen2")
-- p300_mount: location of the p300 pipette mount (default: "left")
+- `dna_plate_loadname`: name of the plate containing DNA to be transformed (default: "armadillo_96_wellplate_200ul_pcr_full_skirt")
+- `dna_plate_slot`: 2
+- `reservoir_loadname`: name of the reservoir containing SOC media and competent cells
+- `reservoir_slot`: 3
+- `transformation_plate_loadname`: name of the plate where transformation occurs (default: "armadillo_96_wellplate_200ul_pcr_full_skirt")
+- `agar_plate_loadname`: name of the agar plate (default: "nunc_singlewell_plate_90ml_4x6_grid")
+- `agar_def_json`: name of the json file with the custom agar plate definition (default: "nunc_singlewell_plate_90ml_4x6_grid")
+- `agar_max_wells_n`: maximum number of wells on the agar plate (default: 24)
+- `agar_slot`: location of the agar plates given as a list (default: [1])
+- `p20_tiprack_loadname`: name of the p20 tiprack (default: "opentrons_96_tiprack_20ul")
+- `p20_tiprack_slot`: location of the p20 tiprack (Default: 6)
+- `p20_name`: name of the p20 pipette (default: "p20_single_gen2")
+- `p20_mount`: location of the p20 pipette mount (default: "right")
+- `p300_tiprack_loadname`: name of the p300 tiprack (default: "opentrons_96_tiprack_300ul")
+- `p300_tiprack_slot`: location of the p300 tiprack (Default: 9)
+- `p300_name`: name of the p300 pipette (default: "p300_multi_gen2")
+- `p300_mount`: location of the p300 pipette mount (default: "left")
 
 
 **Liquid handling settings**
-- dispense_rate: dispense rate of the pipette while spotting in µL/sec (default: 60)
-- aspirate_rate: spirate rate of the pipette while spotting in µL/sec (default: 60)
-- dispense_height: height at which the piepette dispenses above the bottom of the plate in mm (default: 10.2)
+- `dispense_rate`: dispense rate of the pipette while spotting in µL/sec (default: 60)
+- `aspirate_rate`: spirate rate of the pipette while spotting in µL/sec (default: 60)
+- `dispense_height`: height at which the piepette dispenses above the bottom of the plate in mm (default: 10.2)
 
 **Optional**
-- test_dispense_height: test for the dispense height above the agar plate (default: true)
-- test_dispense_height:
-- agar_incubation: agar plate incubation in place on the temperature module (default: false)
-- temp_mod_slot: (default: 4)
-- agar_incubation_temp: set the incubation temperature for the temperature module in celsius (default: 37)
+- `test_dispense_height`: test for the dispense height above the agar plate (default: true)
+- `test_dispense_height`:
+- `agar_incubation`: agar plate incubation in place on the temperature module (default: false)
+- `temp_mod_slot`: (default: 4)
+- `agar_incubation_temp`: set the incubation temperature for the temperature module in celsius (default: 37)
 
 
 ### Opentrons OT2 deck