Merge pull request #28 from flywheel-apps/no-tmp

No tmp

README.md

@@ -51,6 +51,9 @@ to provide the license to this gear.  A license is required for this gear to run
 ### fs-subjects-dir (optional)
 Zip file of existing FreeSurfer subject's directory to reuse.  If the output of FreeSurfer recon-all is provided to fMRIPrep, that output will be used rather than re-running recon-all.  Unzipping the file should produce a particular subject's directory which will be placed in the $FREESURFER_HOME/subjects directory.  The name of the directory must match the -subjid as passed to recon-all.  This version of fMRIPrep uses Freesurfer v6.0.1.
 
+### previous-results (optional)
+Provide previously calculated fMRIPrep output results zip file as in input.  This file will be unzipped into the output directory so that previous results will be used instead of re-calculating them.  This input is provided so that bids-fmriprep can be run incrementally as new data is acquired.
+
 ### work-dir (optional)
 THIS IS A FUTURE OPTIONAL INPUT.  It has not yet been added.  Provide intermediate fMRIPrep results as a zip file.  This file will be unzipped into the work directory so that previous results will be used instead of re-calculating them.  This option is provided so that bids-fmriprep can be run incrementally as new data is acquired.  The zip file to provide can be produced by using the gear-save-intermediate-output configuration option.  You definitely also want to use the fs-subject-dir input (above) so that FreeSurfer won't be run multiple times.
 

manifest.json

@@ -156,6 +156,11 @@
       "description": "Gear will save ALL intermediate output into fmriprep_work_*.zip",
       "type": "boolean"
     },
+    "gear-writable-dir": {
+      "default": "/var/tmp",
+      "description": "Gears expect to be able to write temporary files in /flywheel/v0/.  If this location is not writable (such as when running in Singularity), this path will be used instead.  fMRIPrep creates a large number of files so this disk space should be fast and local.",
+      "type": "string"
+    },
     "ignore": {
       "default": "",
       "description": "Ignore selected aspects of the input dataset to disable corresponding parts of the workflow (a space delimited list)  Possible choices: fieldmaps, slicetiming, sbref",
@@ -303,13 +308,13 @@
     }
   },
   "custom": {
-    "docker-image": "flywheel/bids-fmriprep:1.2.4_20.2.6",
+    "docker-image": "flywheel/bids-fmriprep:1.2.8_20.2.6",
     "flywheel": {
       "suite": "BIDS Apps"
     },
     "gear-builder": {
       "category": "analysis",
-      "image": "flywheel/bids-fmriprep:1.2.4_20.2.6"
+      "image": "flywheel/bids-fmriprep:1.2.8_20.2.6"
     },
     "license": {
       "dependencies": [
@@ -383,5 +388,5 @@
   "name": "bids-fmriprep",
   "source": "https://github.com/nipreps/fmriprep",
   "url": "https://github.com/flywheel-apps/bids-fmriprep/blob/master/README.md",
-  "version": "1.2.4_20.2.6"
+  "version": "1.2.8_20.2.6"
 }